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Changeset 134:ed3a21033188 (2024-10-20)

Previous changeset 133:cec274db51c0 (2024-10-18)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit bb6736899ac3029f73455637a04a006fcd857fc2

modified:
jbrowse2.py
jbrowse2.xml
macros.xml

diff -r cec274db51c0 -r ed3a21033188 blastxml_to_gapped_gff3.py
--- a/blastxml_to_gapped_gff3.py Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,302 +0,0 @@\n-#!/usr/bin/env python\n-import argparse\n-import copy\n-import logging\n-import re\n-import sys\n-\n-from BCBio import GFF\n-\n-logging.basicConfig(level=logging.INFO)\n-log = logging.getLogger(name="blastxml2gff3")\n-\n-__doc__ = """\n-BlastXML files, when transformed to GFF3, do not normally show gaps in the\n-blast hits. This tool aims to fill that "gap".\n-"""\n-\n-\n-def blastxml2gff3(blastxml, min_gap=3, trim=False, trim_end=False, include_seq=False):\n- from Bio.Blast import NCBIXML\n- from Bio.Seq import Seq\n- from Bio.SeqRecord import SeqRecord\n- from Bio.SeqFeature import SeqFeature, SimpleLocation\n-\n- blast_records = NCBIXML.parse(blastxml)\n- for idx_record, record in enumerate(blast_records):\n- # http://www.sequenceontology.org/browser/release_2.4/term/SO:0000343\n- match_type = { # Currently we can only handle BLASTN, BLASTP\n- "BLASTN": "nucleotide_match",\n- "BLASTP": "protein_match",\n- }.get(record.application, "match")\n-\n- recid = record.query\n- if " " in recid:\n- recid = recid[0: recid.index(" ")]\n-\n- rec = SeqRecord(Seq("ACTG"), id=recid)\n- for idx_hit, hit in enumerate(record.alignments):\n- for idx_hsp, hsp in enumerate(hit.hsps):\n- qualifiers = {\n- "ID": "b2g.%s.%s.%s" % (idx_record, idx_hit, idx_hsp),\n- "source": "blast",\n- "score": hsp.expect,\n- "accession": hit.accession,\n- "hit_id": hit.hit_id,\n- "length": hit.length,\n- "hit_titles": hit.title.split(" >"),\n- }\n- if include_seq:\n- qualifiers.update(\n- {\n- "blast_qseq": hsp.query,\n- "blast_sseq": hsp.sbjct,\n- "blast_mseq": hsp.match,\n- }\n- )\n-\n- for prop in (\n- "score",\n- "bits",\n- "identities",\n- "positives",\n- "gaps",\n- "align_length",\n- "strand",\n- "frame",\n- "query_start",\n- "query_end",\n- "sbjct_start",\n- "sbjct_end",\n- ):\n- qualifiers["blast_" + prop] = getattr(hsp, prop, None)\n-\n- desc = hit.title.split(" >")[0]\n- qualifiers["description"] = desc[desc.index(" "):]\n-\n- # This required a fair bit of sketching out/match to figure out\n- # the first time.\n- #\n- # the match_start location must account for queries and\n- # subjecst that start at locations other than 1\n- parent_match_start = hsp.query_start - hsp.sbjct_start\n- # The end is the start + hit.length because the match itself\n- # may be longer than the parent feature, so we use the supplied\n- # subject/hit length to calculate the real ending of the target\n- # protein.\n- parent_match_end = hsp.query_start + hit.length + hsp.query.count("-")\n-\n- # If we trim the left end, we need to trim without losing information.\n- used_parent_match_start = parent_match_start\n- if trim:\n- if parent_match_start < 1:\n- used_parent_match_start = 0\n-\n- if trim or trim_end:\n- if parent_match_end > hsp.query_end:\n- parent_match_end = hsp.query_end + 1\n-\n- # The ``match`` feature will hold one or more ``match_part``s\n- top_feature = SeqFeature(\n- SimpleLocation(used_parent_match_start, parent_match_end, strand=0),\n- '..b' fm += match[prev: position.start()]\n- fs += subject[prev: position.start()]\n- prev = position.start() + 1\n- fq += query[prev:]\n- fm += match[prev:]\n- fs += subject[prev:]\n-\n- return (fq, fm, fs)\n-\n-\n-def generate_parts(query, match, subject, ignore_under=3):\n- region_q = []\n- region_m = []\n- region_s = []\n-\n- (query, match, subject) = __remove_query_gaps(query, match, subject)\n-\n- region_start = -1\n- region_end = -1\n- mismatch_count = 0\n- for i, (q, m, s) in enumerate(zip(query, match, subject)):\n-\n- # If we have a match\n- if m != " " or m == "+":\n- if region_start == -1:\n- region_start = i\n- # It\'s a new region, we need to reset or it\'s pre-seeded with\n- # spaces\n- region_q = []\n- region_m = []\n- region_s = []\n- region_end = i\n- mismatch_count = 0\n- else:\n- mismatch_count += 1\n-\n- region_q.append(q)\n- region_m.append(m)\n- region_s.append(s)\n-\n- if mismatch_count >= ignore_under and region_start != -1 and region_end != -1:\n- region_q = region_q[0:-ignore_under]\n- region_m = region_m[0:-ignore_under]\n- region_s = region_s[0:-ignore_under]\n- yield region_start, region_end + 1, cigar_from_string(\n- region_q, region_m, region_s, strict_m=True\n- )\n- region_q = []\n- region_m = []\n- region_s = []\n-\n- region_start = -1\n- region_end = -1\n- mismatch_count = 0\n-\n- yield region_start, region_end + 1, cigar_from_string(\n- region_q, region_m, region_s, strict_m=True\n- )\n-\n-\n-def _qms_to_matches(query, match, subject, strict_m=True):\n- matchline = []\n-\n- for (q, m, s) in zip(query, match, subject):\n- ret = ""\n-\n- if m != " " or m == "+":\n- ret = "="\n- elif m == " ":\n- if q == "-":\n- ret = "D"\n- elif s == "-":\n- ret = "I"\n- else:\n- ret = "X"\n- else:\n- log.warn("Bad data: \\n\\t%s\\n\\t%s\\n\\t%s\\n" % (query, match, subject))\n-\n- if strict_m:\n- if ret == "=" or ret == "X":\n- ret = "M"\n-\n- matchline.append(ret)\n- return matchline\n-\n-\n-def _matchline_to_cigar(matchline):\n- cigar_line = []\n- last_char = matchline[0]\n- count = 0\n- for char in matchline:\n- if char == last_char:\n- count += 1\n- else:\n- cigar_line.append("%s%s" % (last_char, count))\n- count = 1\n- last_char = char\n- cigar_line.append("%s%s" % (last_char, count))\n- return " ".join(cigar_line)\n-\n-\n-def cigar_from_string(query, match, subject, strict_m=True):\n- matchline = _qms_to_matches(query, match, subject, strict_m=strict_m)\n- if len(matchline) > 0:\n- return _matchline_to_cigar(matchline)\n- else:\n- return ""\n-\n-\n-if __name__ == "__main__":\n- parser = argparse.ArgumentParser(\n- description="Convert Blast XML to gapped GFF3", epilog=""\n- )\n- parser.add_argument(\n- "blastxml", type=argparse.FileType("r"), help="Blast XML Output"\n- )\n- parser.add_argument(\n- "--min_gap",\n- type=int,\n- help="Maximum gap size before generating a new match_part",\n- default=3,\n- )\n- parser.add_argument(\n- "--trim",\n- action="store_true",\n- help="Trim blast hits to be only as long as the parent feature",\n- )\n- parser.add_argument(\n- "--trim_end",\n- action="store_true",\n- help="Cut blast results off at end of gene",\n- )\n- parser.add_argument("--include_seq", action="store_true", help="Include sequence")\n- args = parser.parse_args()\n-\n- for rec in blastxml2gff3(**vars(args)):\n- if len(rec.features):\n- GFF.write([rec], sys.stdout)\n'

diff -r cec274db51c0 -r ed3a21033188 filter_multihit_paf.py
--- a/filter_multihit_paf.py Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,94 +0,0 @@
-# idea from https://github.com/marbl/MashMap/blob/master/scripts/denovo_repeat_annotation.py
-# adds filter for more than minMatch denovo repeated paf read locations: >1 gives ~13%, >3 gives 3% of all hits in testing a big and small paf.
-# A haplotype paf filtered of denovo repeats might give cleaner dotplots, because they add visual noise and repeats are less informative for sequence similarity.
-# Alternative to use repeatmasked haplotype as the mashmap reference might also be useful.
-# Also outputs a bed with the multimatch regions filtered from the paf with their repeat count as the score
-# ross lazarus october 6 2024
-
-import argparse
-
-from collections import OrderedDict
-
-
-def pafDeDupe(inPaf, outDeNovoBed, outPaf, minMatch):
-    """
-    Usage notes:
-    if a segment appears more than once on the left of a paf row, it can be considered a denovo repeat!
-    Contig and start offset are used as the id so approximate-ish.
-    Seems a consistent 13% 1+ denovo repeats with different levels of identity and match length
-    3+ finds a much lower 3% of hits
-
-    With a 181217 row squirrelhaps1k.paf at 1k 99%, get about 13% denovo repeat rows
-    (venv311) ross@pn50:~/rossgit/galaxytools/tools/jbrowse2$ python filter_multihit_paf.py --inpaf squirrelhaps1k.paf --outbed sh1k.bed --outpaf sh1kdedupe.paf --minMatch 1
-    (venv311) ross@pn50:~/rossgit/galaxytools/tools/jbrowse2$ wc -l sh1kdedupe.paf
-    109179 sh1kdedupe.paf
-    (venv311) ross@pn50:~/rossgit/galaxytools/tools/jbrowse2$ wc -l sh1k.bed
-    23015 sh1k.bed
-
-    venv311) ross@pn50:~/rossgit/galaxytools/tools/jbrowse2$ python filter_multihit_paf.py --inpaf squirrelhaps1k.paf --outbed sh1k.bed --outpaf sh1kdedupe.paf --minMatch 3
-    (venv311) ross@pn50:~/rossgit/galaxytools/tools/jbrowse2$ wc -l sh1k.bed
-    7996 sh1k.bed
-
-    with a smaller 26610 10k 95%, get about
-    (venv3row 11) ross@pn50:~/rossgit/galaxytools/tools/jbrowse2$ wc -l squirrelhaps.paf
-    26610 squirrelhaps.paf
-    (venv311) ross@pn50:~/rossgit/galaxytools/tools/jbrowse2$ python filter_multihit_paf.py squirrelhaps.paf sh.bed shdedupe.paf
-    (venv311) ross@pn50:~/rossgit/galaxytools/tools/jbrowse2$ wc -l shdedupe.paf
-    18332 shdedupe.paf
-    (venv311) ross@pn50:~/rossgit/galaxytools/tools/jbrowse2$ wc -l sh.bed
-    3663 sh.bed
-    """
-
-    CHROMOSOMECOL1 = 0
-    STARTCOL1 = 2
-    ENDCOL1 = 3
-    hitTable1 = OrderedDict()
-    hitTable1_lens = {}
-    filterLen = minMatch
-    minMatch = int(minMatch)
-    filterMe = {}
-
-    with open(inPaf) as f:
-        for i, line in enumerate(f):
-            rowElements = line.split()
-            chromosome1 = rowElements[CHROMOSOMECOL1]
-            start1 = int(rowElements[STARTCOL1])
-            end1 = int(rowElements[ENDCOL1])
-            h1key = "%s~%d" % (chromosome1, start1)
-            if hitTable1.get(h1key, None):
-                hitTable1[h1key].append(i)
-                if len(hitTable1[h1key]) > minMatch:
-                    filterMe[i] = i
-            else:
-                hitTable1[h1key] = [
-                    i,
-                ]
-                hitTable1_lens[h1key] = abs(end1 - start1)
-    with open(outDeNovoBed, "w") as f:
-        for k in hitTable1.keys():
-            # OrderedDict so input paf order preserved - if that's wrong so is the bed.
-            nk = len(hitTable1[k])
-            if nk > minMatch:
-                (chr, start) = k.split("~")
-                end = int(start) + hitTable1_lens.get(k, 0)
-                name= '_'.join([chr,start])
-                row = (chr, start, "%d" % end, name, "%d" % nk)
-                f.write("\t".join(row))
-                f.write("\n")
-    with open(outPaf, "w") as f:
-        f.writelines(
-        line for i, line in enumerate(open(inPaf)) if not filterMe.get(i, None)
-    )
-
-
-if __name__ == "__main__":
-    VERS = 0.01
-    parser = argparse.ArgumentParser()
-    a = parser.add_argument
-    a("--inpaf", default=None)
-    a("--outbed", default=None)
-    a("--outpaf", default=None)
-    a("--minmatch", default=1, type=int)
-    a('--version', action='version', version='%(prog)s 0.1')
-    args = parser.parse_args()
-    pafDeDupe(args.inpaf, args.outbed, args.outpaf, args.minmatch)

diff -r cec274db51c0 -r ed3a21033188 gff3_rebase.py
--- a/gff3_rebase.py Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,194 +0,0 @@\n-#!/usr/bin/env python\n-import argparse\n-import copy\n-import logging\n-import sys\n-\n-from BCBio import GFF\n-from Bio.SeqFeature import FeatureLocation\n-\n-logging.basicConfig(level=logging.INFO)\n-log = logging.getLogger(__name__)\n-\n-__author__ = "Eric Rasche"\n-__version__ = "0.4.0"\n-__maintainer__ = "Eric Rasche"\n-__email__ = "esr@tamu.edu"\n-\n-\n-def feature_lambda(feature_list, test, test_kwargs, subfeatures=True):\n- """Recursively search through features, testing each with a test function, yielding matches.\n-\n- GFF3 is a hierachical data structure, so we need to be able to recursively\n- search through features. E.g. if you\'re looking for a feature with\n- ID=\'bob.42\', you can\'t just do a simple list comprehension with a test\n- case. You don\'t know how deeply burried bob.42 will be in the feature tree. This is where feature_lambda steps in.\n-\n- :type feature_list: list\n- :param feature_list: an iterable of features\n-\n- :type test: function reference\n- :param test: a closure with the method signature (feature, **kwargs) where\n- the kwargs are those passed in the next argument. This\n- function should return True or False, True if the feature is\n- to be yielded as part of the main feature_lambda function, or\n- False if it is to be ignored. This function CAN mutate the\n- features passed to it (think "apply").\n-\n- :type test_kwargs: dictionary\n- :param test_kwargs: kwargs to pass to your closure when it is called.\n-\n- :type subfeatures: boolean\n- :param subfeatures: when a feature is matched, should just that feature be\n- yielded to the caller, or should the entire sub_feature\n- tree for that feature be included? subfeatures=True is\n- useful in cases such as searching for a gene feature,\n- and wanting to know what RBS/Shine_Dalgarno_sequences\n- are in the sub_feature tree (which can be accomplished\n- with two feature_lambda calls). subfeatures=False is\n- useful in cases when you want to process (and possibly\n- return) the entire feature tree, such as applying a\n- qualifier to every single feature.\n-\n- :rtype: yielded list\n- :return: Yields a list of matching features.\n- """\n- # Either the top level set of [features] or the subfeature attribute\n- for feature in feature_list:\n- if test(feature, **test_kwargs):\n- if not subfeatures:\n- feature_copy = copy.deepcopy(feature)\n- feature_copy.sub_features = []\n- yield feature_copy\n- else:\n- yield feature\n-\n- if hasattr(feature, \'sub_features\'):\n- for x in feature_lambda(feature.sub_features, test, test_kwargs, subfeatures=subfeatures):\n- yield x\n-\n-\n-def feature_test_qual_value(feature, **kwargs):\n- """Test qualifier values.\n-\n- For every feature, check that at least one value in\n- feature.quailfiers(kwargs[\'qualifier\']) is in kwargs[\'attribute_list\']\n- """\n- for attribute_value in feature.qualifiers.get(kwargs[\'qualifier\'], []):\n- if attribute_value in kwargs[\'attribute_list\']:\n- return True\n- return False\n-\n-\n-def __get_features(child, interpro=False):\n- child_features = {}\n- for rec in GFF.parse(child):\n- # Only top level\n- for feature in rec.features:\n- # Get the record id as parent_feature_id (since this is how it will be during remapping)\n- parent_feature_id = rec.id\n- # If it\'s an interpro specific gff3 file\n- if interpro:\n- # Then we ignore polypeptide features as they\'re useless\n- if feature.type == \'polypeptide\':\n- continue\n- # If there\'s an undersco'..b' # I do not know the rationale for this, removing.\n- # if \'_\' in parent_feature_id:\n- # parent_feature_id = parent_feature_id[parent_feature_id.index(\'_\') + 1:]\n-\n- try:\n- child_features[parent_feature_id].append(feature)\n- except KeyError:\n- child_features[parent_feature_id] = [feature]\n- # Keep a list of feature objects keyed by parent record id\n- return child_features\n-\n-\n-def __update_feature_location(feature, parent, protein2dna):\n- start = feature.location.start\n- end = feature.location.end\n- if protein2dna:\n- start *= 3\n- end *= 3\n-\n- if parent.location.strand >= 0:\n- ns = parent.location.start + start\n- ne = parent.location.start + end\n- st = +1\n- else:\n- ns = parent.location.end - end\n- ne = parent.location.end - start\n- st = -1\n-\n- # Don\'t let start/stops be less than zero. It\'s technically valid for them\n- # to be (at least in the model I\'m working with) but it causes numerous\n- # issues.\n- #\n- # Instead, we\'ll replace with %3 to try and keep it in the same reading\n- # frame that it should be in.\n- if ns < 0:\n- ns %= 3\n- if ne < 0:\n- ne %= 3\n-\n- feature.location = FeatureLocation(ns, ne, strand=st)\n-\n- if hasattr(feature, \'sub_features\'):\n- for subfeature in feature.sub_features:\n- __update_feature_location(subfeature, parent, protein2dna)\n-\n-\n-def rebase(parent, child, interpro=False, protein2dna=False, map_by=\'ID\'):\n- # get all of the features we will be re-mapping in a dictionary, keyed by parent feature ID\n- child_features = __get_features(child, interpro=interpro)\n-\n- for rec in GFF.parse(parent):\n- replacement_features = []\n- for feature in feature_lambda(\n- rec.features,\n- # Filter features in the parent genome by those that are\n- # "interesting", i.e. have results in child_features array.\n- # Probably an unnecessary optimisation.\n- feature_test_qual_value,\n- {\n- \'qualifier\': map_by,\n- \'attribute_list\': child_features.keys(),\n- },\n- subfeatures=False):\n-\n- # Features which will be re-mapped\n- to_remap = child_features[feature.id]\n- # TODO: update starts\n- fixed_features = []\n- for x in to_remap:\n- # Then update the location of the actual feature\n- __update_feature_location(x, feature, protein2dna)\n-\n- if interpro:\n- for y in (\'status\', \'Target\'):\n- try:\n- del x.qualifiers[y]\n- except Exception:\n- pass\n-\n- fixed_features.append(x)\n- replacement_features.extend(fixed_features)\n- # We do this so we don\'t include the original set of features that we\n- # were rebasing against in our result.\n- rec.features = replacement_features\n- rec.annotations = {}\n- GFF.write([rec], sys.stdout)\n-\n-\n-if __name__ == \'__main__\':\n- parser = argparse.ArgumentParser(description=\'rebase gff3 features against parent locations\', epilog="")\n- parser.add_argument(\'parent\', type=argparse.FileType(\'r\'), help=\'Parent GFF3 annotations\')\n- parser.add_argument(\'child\', type=argparse.FileType(\'r\'), help=\'Child GFF3 annotations to rebase against parent\')\n- parser.add_argument(\'--interpro\', action=\'store_true\',\n- help=\'Interpro specific modifications\')\n- parser.add_argument(\'--protein2dna\', action=\'store_true\',\n- help=\'Map protein translated results to original DNA data\')\n- parser.add_argument(\'--map_by\', help=\'Map by key\', default=\'ID\')\n- args = parser.parse_args()\n- rebase(**vars(args))\n'

diff -r cec274db51c0 -r ed3a21033188 jbrowse2.py
--- a/jbrowse2.py Fri Oct 18 11:57:55 2024 +0000
+++ b/jbrowse2.py Sun Oct 20 07:11:16 2024 +0000

[

b'@@ -13,7 +13,6 @@\n import string\n import struct\n import subprocess\n-import tempfile\n import urllib.request\n import xml.etree.ElementTree as ET\n from collections import defaultdict\n@@ -446,7 +445,7 @@\n p = subprocess.Popen(\n command,\n cwd=self.outdir,\n- shell=False,\n+ shell=True,\n stdin=subprocess.PIPE,\n stdout=subprocess.PIPE,\n stderr=subprocess.PIPE,\n@@ -554,9 +553,8 @@\n else:\n faname = gname + ".fa.gz"\n fadest = os.path.realpath(os.path.join(self.outdir, faname))\n- cmd = ["bgzip", "-i", "-c", fapath, "-I", fadest + ".gzi"]\n- with open(fadest, "wb") as fout:\n- self.subprocess_check_call(cmd, output=fout)\n+ cmd = "bgzip -k -i -c -I \'%s.gzi\' \'%s\' > \'%s\'" % (fadest, fapath, fadest)\n+ subprocess.run(cmd, shell=True)\n cmd = ["samtools", "faidx", fadest]\n self.subprocess_check_call(cmd)\n contig = open(fadest + ".fai", "r").readline().strip()\n@@ -753,38 +751,59 @@\n else:\n self.config_json.update(mafPlugin)\n \n- def _blastxml_to_gff3(self, xml, min_gap=10):\n- gff3_unrebased = tempfile.NamedTemporaryFile(delete=False)\n- cmd = [\n- "python",\n- os.path.join(INSTALLED_TO, "blastxml_to_gapped_gff3.py"),\n- "--trim",\n- "--trim_end",\n- "--include_seq",\n- "--min_gap",\n- str(min_gap),\n- xml,\n- ]\n- subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_unrebased)\n- gff3_unrebased.close()\n- logging.debug("### blastxml to gff3 cmd = %s" % " ".join(cmd))\n- return gff3_unrebased.name\n+ def _sort_gff(self, data, dest):\n+ # Only index if not already done\n+ if not os.path.exists(dest):\n+ e = os.environ\n+ e["SHELL"] = "/bin/sh"\n+ cmd = "jbrowse sort-gff %s | bgzip -c > %s" % (data, dest)\n+ subprocess.run(cmd, env=e, shell=True)\n+ self.subprocess_check_call(["tabix", "-f", "-p", "gff", dest])\n \n- def add_blastxml(self, data, trackData, blastOpts, **kwargs):\n- gff3 = self._blastxml_to_gff3(data, min_gap=blastOpts["min_gap"])\n- if "parent" in blastOpts and blastOpts["parent"] != "None":\n- gff3_rebased = tempfile.NamedTemporaryFile(delete=False)\n- cmd = ["python", os.path.join(INSTALLED_TO, "gff3_rebase.py")]\n- if blastOpts.get("protein", "false") == "true":\n- cmd.append("--protein2dna")\n- cmd.extend([os.path.realpath(blastOpts["parent"]), gff3])\n- subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_rebased)\n- logging.debug("### gff3rebase cmd = %s" % " ".join(cmd))\n- gff3_rebased.close()\n- # Replace original gff3 file\n- shutil.copy(gff3_rebased.name, gff3)\n- os.unlink(gff3_rebased.name)\n- self.add_gff(gff3, trackData, **kwargs)\n+ def add_gff(self, data, trackData):\n+ tId = trackData["label"]\n+ useuri = trackData["useuri"].lower() == "yes"\n+ if useuri:\n+ url = trackData["path"]\n+ else:\n+ url = tId + ".gz"\n+ dest = os.path.join(self.outdir, url)\n+ self._sort_gff(data, dest)\n+ categ = trackData["category"]\n+ trackDict = {\n+ "type": "FeatureTrack",\n+ "trackId": tId,\n+ "name": trackData["name"],\n+ "assemblyNames": [trackData["assemblyNames"]],\n+ "category": [\n+ categ,\n+ ],\n+ "adapter": {\n+ "type": "Gff3TabixAdapter",\n+ "gffGzLocation": {\n+ "uri": url,\n+ },\n+ "index": {\n+ "location": {\n+ "uri": url + ".tbi",\n+ }\n+ },\n+ },\n+ '..b'self, data, dest):\n- # Only index if not already done\n- if not os.path.exists(dest):\n- e = os.environ\n- e[\'SHELL\'] = \'/bin/sh\'\n- cmd = [\'/bin/sh\', \'-c\', "jbrowse sort-gff %s | bgzip -c > %s" % (data, dest)]\n- subprocess.run(cmd, env=e)\n- self.subprocess_check_call(["tabix", "-f", "-p", "gff", dest])\n-\n def _sort_bed(self, data, dest):\n # Only index if not already done\n if not os.path.exists(dest):\n@@ -1017,51 +1027,6 @@\n cmd = ["tabix", "-f", "-p", "bed", dest]\n self.subprocess_check_call(cmd)\n \n- def add_gff(self, data, trackData):\n- tId = trackData["label"]\n- useuri = trackData["useuri"].lower() == "yes"\n- if useuri:\n- url = trackData["path"]\n- else:\n- url = tId + ".gz"\n- dest = os.path.join(self.outdir, url)\n- self._sort_gff(data, dest)\n- categ = trackData["category"]\n- trackDict = {\n- "type": "FeatureTrack",\n- "trackId": tId,\n- "name": trackData["name"],\n- "assemblyNames": [trackData["assemblyNames"]],\n- "category": [\n- categ,\n- ],\n- "adapter": {\n- "type": "Gff3TabixAdapter",\n- "gffGzLocation": {\n- "uri": url,\n- },\n- "index": {\n- "location": {\n- "uri": url + ".tbi",\n- }\n- },\n- },\n- "displays": [\n- {\n- "type": "LinearBasicDisplay",\n- "displayId": "%s-LinearBasicDisplay" % tId,\n- },\n- {\n- "type": "LinearArcDisplay",\n- "displayId": "%s-LinearArcDisplay" % tId,\n- },\n- ],\n- }\n- style_json = self._prepare_track_style(trackDict)\n- trackDict["style"] = style_json\n- self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict))\n- self.trackIdlist.append(tId)\n-\n def add_bed(self, data, ext, trackData):\n bedPlugin = {"name": "BedScorePlugin", "umdLoc": {"uri": "bedscoreplugin.js"}}\n tId = trackData["label"]\n@@ -1139,7 +1104,7 @@\n useuri = data.startswith("http://") or data.startswith("https://")\n if not useuri:\n if canPIF:\n- fakeName = "%s.paf" % tId\n+ fakeName = os.path.join(self.outdir, "%s.paf" % tId)\n url = "%s.pif.gz" % tId\n cmd = ["cp", data, fakeName]\n self.subprocess_check_call(cmd)\n@@ -1147,7 +1112,7 @@\n "jbrowse",\n "make-pif",\n fakeName,\n- ] # jbrowse pif input.paf --out output.pif.gz # specify output file, creates output.pif.gz.tbi also\n+ ]\n self.subprocess_check_call(cmd)\n usePIF = True\n else:\n@@ -1160,7 +1125,7 @@\n categ = trackData["category"]\n pg = pafOpts["genome"].split(",")\n pgc = [x.strip() for x in pg if x.strip() > ""]\n- gnomes = [x.split(" ~ ") for x in pgc]\n+ gnomes = [x.split("~~~") for x in pgc]\n logging.debug("pg=%s, gnomes=%s" % (pg, gnomes))\n passnames = [trackData["assemblyNames"]] # always first\n for i, (gpath, gname) in enumerate(gnomes):\n@@ -1336,12 +1301,6 @@\n outputTrackConfig,\n cram_indexes=real_indexes,\n )\n- elif dataset_ext == "blastxml":\n- self.add_blastxml(\n- dataset_path,\n- outputTrackConfig,\n- track["conf"]["options"]["blast"],\n- )\n elif dataset_ext == "vcf":\n self.add_vcf(dataset_path, outputTrackConfig)\n elif dataset_ext == "paf":\n'

diff -r cec274db51c0 -r ed3a21033188 jbrowse2.xml
--- a/jbrowse2.xml Fri Oct 18 11:57:55 2024 +0000
+++ b/jbrowse2.xml Sun Oct 20 07:11:16 2024 +0000

[

b'@@ -10,9 +10,7 @@\n <expand macro="requirements"/>\n <required_files>\n <include path="autogenJB2.py"/>\n- <include path="blastxml_to_gapped_gff3.py"/>\n <include path="convertMAF.sh"/>\n- <include path="gff3_rebase.py"/>\n <include path="jb2_webserver.py"/>\n <include path="jbrowse2.py"/>\n <include path="maf2bed.py"/>\n@@ -100,10 +98,10 @@\n </metadata>\n </genome>\n #else if str($assembly.reference_genome.genome_type_select) == "indexed":\n- <genome path="${assembly.reference_genome.genome.fields.path}" label="${assembly.reference_genome.genome.fields.dbkey}" useuri="no">\n+ <genome path="${assembly.reference_genome.indexed.fields.path}" label="${assembly.reference_genome.indexed.fields.dbkey}" useuri="no">\n <metadata>\n <dataset\n- dname = "${assembly.reference_genome.genome.fields.name}" />\n+ dname = "${assembly.reference_genome.indexed.fields.name}" />\n </metadata>\n </genome>\n #else\n@@ -214,7 +212,7 @@\n #if $input_exists == "True":\n <options>\n <style>\n- #if str($track.data_format.data_format_select) in ["gff", "bed", "maf", "blastxml"]:\n+ #if str($track.data_format.data_format_select) in ["gff", "bed", "maf"]:\n <type>${track.data_format.jbstyle.display}</type>\n #if str($track.data_format.jbstyle.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]:\n <trackShowLabels>${track.data_format.jbstyle.show_labels}</trackShowLabels>\n@@ -246,29 +244,25 @@\n #end if\n </style>\n #if str($track.data_format.data_format_select) == "bam":\n- <bam>\n- <bam_index>\n- #for $dataset in $track.data_format.useuri.annotation:\n- ${dataset} ~ ${dataset.metadata.bam_index},\n- #end for\n- </bam_index>\n- </bam>\n+ #if str($track.data_format.useuri.insource) == "history":\n+ <bam>\n+ <bam_index>\n+ #for $dataset in $track.data_format.useuri.annotation:\n+ ${dataset}~~~${dataset.metadata.bam_index},\n+ #end for\n+ </bam_index>\n+ </bam>\n+ #end if\n #else if str($track.data_format.data_format_select) == "cram":\n- <cram>\n- <cram_index>\n- #for $dataset in $track.data_format.useuri.annotation:\n- ${dataset} ~ ${dataset.metadata.cram_index},\n- #end for\n- </cram_index>\n- </cram>\n- #else if str($track.data_format.data_format_select) == "blastxml":\n- <blast>\n- #if str($track.data_format.blast_parent) != "":\n- <parent>${track.data_format.blast_parent}</parent>\n- #end if\n- <protein>${track.data_format.is_protein}</protein>\n- <min_gap>${track.data_format.min_gap}</min_gap>\n- </blast>\n+ #if str($track.data_format.useuri.insource) == "history":\n+ '..b' </repeat>\n <repeat name="refuri">\n- <param name="annotation" value="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Vvinifera1.fa.gz"/>\n- <param name="annoname" value="Vvinifera1.URI"/>\n+ <param name="uri" value="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Vvinifera1.fa.gz"/>\n+ <param name="refname" value="Vvinifera1.URI"/>\n </repeat>\n </conditional>\n </conditional>\n@@ -643,7 +614,7 @@\n </section>\n <output name="output" ftype="zip">\n <assert_contents>\n- <has_archive_member path=".*" n="678" delta="10"/>\n+ <has_archive_member path=".*" n="676" delta="10"/>\n <has_archive_member path="index.html"/>\n <has_archive_member path="manifest.json">\n <has_text text="favicon.ico"/>\n@@ -665,10 +636,9 @@\n <has_archive_member path="merlin-sample.bam_5"/>\n <has_archive_member path="merlin-sample.bam_5.bai"/>\n <has_archive_member path="merlinlastz.maf_6.sorted.bed.gz.tbi"/>\n- <has_archive_member path="merlin.blastxml_7.gz"/>\n- <has_archive_member path="dm3test.cool_9.hic"/>\n- <has_archive_member path="peach-grape-map.paf_10"/>\n- <has_archive_member path="arabgrapepeach.paf_11"/>\n+ <has_archive_member path="dm3test.cool_7.hic"/>\n+ <has_archive_member path="peach-grape-map.paf_8"/>\n+ <has_archive_member path="arabgrapepeach.paf_10"/>\n <has_archive_member path="Merlin.fa.gz.fai"/>\n <has_archive_member path="dm3.fa.fa.gz.fai"/>\n <has_archive_member path="Ppersica1.fa.fa.gz"/>\n@@ -1199,7 +1169,6 @@\n bam\n bed\n bigwig\n- blastxml\n cram\n gff3\n hic\n@@ -1207,6 +1176,7 @@\n paf\n vcf\n \n+Blastxml was deprecated in JBrowse 2.15.4 because the emitted GFF fails validation and will not display\n Note that cram and bam will be large, so very slow amd are only recommended if you need the cigar annotation. Otherwise conversion to bed is recommended to slim them down. \n Unfortunately if you have millions of rows in a bed, it will also be very slow - in which case a bigwig is recommended. \n \n@@ -1283,26 +1253,8 @@\n BlastXML\n ~~~~~~~~\n \n-JiG now supports both blastn and blastp datasets. JiG internally uses a\n-blastXML to gapped GFF3 tool to convert your blastxml datasets into a\n-format amenable to visualization in JBrowse. This tool is also\n-available separately from the IUC on the toolshed.\n-\n-**Minimum Gap Size** reflects how long a gap must be before it becomes a\n-real gap in the processed gff3 file. In the picture above, various sizes\n-of gaps can be seen. If the minimum gap size was set much higher, say\n-100nt, many of the smaller gaps would disappear, and the features on\n-both sides would be merged into one, longer feature. This setting is\n-inversely proportional to runtime and output file size. *Do not set this\n-to a low value for large datasets*. By setting this number lower, you\n-will have extremely large outputs and extremely long runtimes. The\n-default was configured based off of the author\'s experience, but the\n-author only works on small viruses. It is *strongly* recommended that\n-you filter your blast results before display, e.g. picking out the top\n-10 hits or so.\n-\n-**Protein blast search** option merely informs underlying tools that\n-they should adjust feature locations by 3x.\n+Deprecated in 2.15.4 because the new GFF parser rejects the output of the \n+original JBrowse1 blastxml to gff converter. \n \n Local viewing\n =============\n'

diff -r cec274db51c0 -r ed3a21033188 macros.xml
--- a/macros.xml Fri Oct 18 11:57:55 2024 +0000
+++ b/macros.xml Sun Oct 20 07:11:16 2024 +0000

@@ -449,10 +449,11 @@
             </when>
             <when value="uri">
                 <param name="annouri" type="text" label="@LABEL@" help="Requires internet. Will show an error if not online. Saves all the tabix file disk storage"/>
-                <param name="annoname" type="text" label="Short name for track display">
-                    <sanitizer invalid_char="_">
-                        <valid initial="string.printable">
-                            <remove value="'"/>
+                <param name="annoname" type="text" label="Short name for track display. Letters, numbers, - and _ only">
+                    <sanitizer invalid_char="">
+                        <valid initial="string.ascii_letters,string.digits">
+                            <add value="_"/>
+                            <add value="-"/>
                         </valid>
                     </sanitizer>
                 </param>
@@ -470,11 +471,12 @@
             </when>
             <when value="uri">
                 <repeat name="refuri" title="PAF reference comparison genome URI" min="1">
-                    <param name="annotation" type="text" label="@LABEL@"/>
-                    <param name="annoname" type="text" label="Short name for this reference" help="Short names take less track space">
-                        <sanitizer invalid_char="_">
-                            <valid initial="string.printable">
-                                <remove value="'"/>
+                    <param name="uri" type="text" label="@LABEL@"/>
+                    <param name="refname" type="text" label="Short name for this reference. Letters, numbers, - and _ only" help="Short names take less track space">
+                        <sanitizer invalid_char="">
+                            <valid initial="string.ascii_letters,string.digits">
+                                <add value="_"/>
+                                <add value="-"/>
                             </valid>
                         </sanitizer>
                     </param>

diff -r cec274db51c0 -r ed3a21033188 shdedupe.paf
--- a/shdedupe.paf Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,18267 +0,0 @@\n-SUPER_1\t284260672\t0\t320000\t+\tSUPER_1\t284047837\t98230\t420795\t19\t322565\t28\tid:f:0.998281\tkc:f:1.03157\n-SUPER_1\t284260672\t330000\t480000\t+\tSUPER_1\t284047837\t424255\t574701\t18\t150446\t25\tid:f:0.996963\tkc:f:1.01113\n-SUPER_1\t284260672\t480000\t520000\t-\tSUPER_1\t284047837\t937729\t977715\t15\t40000\t21\tid:f:0.992398\tkc:f:0.942085\n-SUPER_1\t284260672\t530000\t580000\t-\tSUPER_1\t284047837\t877563\t927910\t16\t50347\t21\tid:f:0.992207\tkc:f:0.942731\n-SUPER_1\t284260672\t610000\t640000\t-\tSUPER_7\t168114946\t84471238\t84499671\t5\t30000\t13\tid:f:0.954937\tkc:f:0.945027\n-SUPER_1\t284260672\t690000\t710000\t+\tScaffold_65\t2787905\t1101363\t1121292\t4\t20000\t14\tid:f:0.959515\tkc:f:1.33975\n-SUPER_1\t284260672\t710000\t750000\t-\tSUPER_1\t284047837\t838794\t875196\t14\t40000\t18\tid:f:0.983347\tkc:f:1.02148\n-SUPER_1\t284260672\t760000\t990000\t-\tSUPER_1\t284047837\t596138\t829936\t18\t233798\t25\tid:f:0.996715\tkc:f:0.999644\n-SUPER_1\t284260672\t990000\t1110000\t+\tSUPER_1\t284047837\t956492\t1078127\t17\t121635\t25\tid:f:0.996761\tkc:f:1.02788\n-SUPER_1\t284260672\t1110000\t1570000\t+\tSUPER_1\t284047837\t1111281\t1566885\t20\t460000\t23\tid:f:0.995018\tkc:f:0.993199\n-SUPER_1\t284260672\t1620000\t1690000\t+\tSUPER_1\t284047837\t1548178\t1626468\t12\t78290\t21\tid:f:0.992495\tkc:f:0.90286\n-SUPER_1\t284260672\t1690000\t1970000\t+\tSUPER_1\t284047837\t1636844\t1909245\t19\t280000\t21\tid:f:0.991603\tkc:f:0.903312\n-SUPER_1\t284260672\t1970000\t2390000\t+\tSUPER_1\t284047837\t2006207\t2429696\t20\t423489\t23\tid:f:0.994519\tkc:f:1.00363\n-SUPER_1\t284260672\t2440000\t6310000\t+\tSUPER_1\t284047837\t2426480\t6297055\t18\t3870575\t24\tid:f:0.995572\tkc:f:1.04758\n-SUPER_1\t284260672\t6310000\t8640000\t+\tSUPER_1\t284047837\t6307372\t8635465\t20\t2330000\t23\tid:f:0.994465\tkc:f:1.03554\n-SUPER_1\t284260672\t8650000\t10810000\t+\tSUPER_1\t284047837\t8638716\t10808910\t20\t2170194\t23\tid:f:0.995129\tkc:f:1.04746\n-SUPER_1\t284260672\t10820000\t11990000\t+\tSUPER_1\t284047837\t10816586\t12011044\t20\t1194458\t23\tid:f:0.994622\tkc:f:1.05435\n-SUPER_1\t284260672\t12000000\t14800000\t+\tSUPER_1\t284047837\t12012866\t14821273\t18\t2808407\t24\tid:f:0.995975\tkc:f:1.04085\n-SUPER_1\t284260672\t14790000\t14830000\t-\tSUPER_1\t284047837\t14901975\t14940137\t8\t40000\t20\tid:f:0.988954\tkc:f:0.897274\n-SUPER_1\t284260672\t14830000\t14910000\t-\tSUPER_1\t284047837\t14803615\t14882610\t14\t80000\t17\tid:f:0.978779\tkc:f:0.916787\n-SUPER_1\t284260672\t14850000\t14860000\t+\tSUPER_1\t284047837\t15038599\t15048599\t14\t10000\t20\tid:f:0.989833\tkc:f:1.05855\n-SUPER_1\t284260672\t14860000\t14870000\t+\tSUPER_1\t284047837\t14898244\t14908244\t15\t10000\t23\tid:f:0.994996\tkc:f:0.967711\n-SUPER_1\t284260672\t14910000\t14920000\t+\tSUPER_1\t284047837\t14875769\t14885769\t5\t10000\t14\tid:f:0.95711\tkc:f:0.596396\n-SUPER_1\t284260672\t14920000\t16330000\t+\tSUPER_1\t284047837\t15171069\t16583035\t16\t1411966\t24\tid:f:0.996207\tkc:f:1.04116\n-SUPER_1\t284260672\t16330000\t16340000\t+\tSUPER_10\t143430727\t117284234\t117294234\t11\t10000\t20\tid:f:0.989279\tkc:f:0.86098\n-SUPER_1\t284260672\t16340000\t25580000\t+\tSUPER_1\t284047837\t16583565\t25794868\t13\t9240000\t25\tid:f:0.996547\tkc:f:1.03943\n-SUPER_1\t284260672\t25590000\t26590000\t+\tSUPER_1\t284047837\t25797929\t26797991\t20\t1000062\t24\tid:f:0.996367\tkc:f:1.00571\n-SUPER_1\t284260672\t26590000\t26600000\t+\tSUPER_7\t168114946\t49298008\t49308008\t4\t10000\t15\tid:f:0.970976\tkc:f:0.751408\n-SUPER_1\t284260672\t26600000\t29060000\t+\tSUPER_1\t284047837\t26802503\t29256762\t16\t2460000\t23\tid:f:0.994678\tkc:f:1.06424\n-SUPER_1\t284260672\t29060000\t29070000\t+\tScaffold_6183\t49162\t26040\t36040\t10\t10000\t17\tid:f:0.980634\tkc:f:0.77982\n-SUPER_1\t284260672\t29070000\t31060000\t+\tSUPER_1\t284047837\t29260181\t31256605\t19\t1996424\t23\tid:f:0.994404\tkc:f:1.07323\n-SUPER_1\t284260672\t31060000\t33820000\t+\tSUPER_1\t284047837\t31269848\t34045825\t17\t2775977\t24\tid:f:0.996081\tkc:f:1.04608\n-SUPER_1\t284260672\t33830000\t33860000\t+\tSUPER_1\t284047837\t34045010\t34075442\t19\t30432\t21\tid:f:0.991427\tkc:f:1.17575\n-SUPER_1\t284260672\t33870000\t36860000\t+\tSUPER_1\t284047837\t34081214\t37062652\t15\t2990000\t24\tid:f:0.996004\tkc:f:1.053\n-SUPER_1\t284260672\t36870000\t37990000\t+\tSUPER_1\t284047837\t37065393\t38202739\t17\t1137346\t25\tid:f:0.997011\tkc:f:1.03521\n-SUPER_1\t284260672\t38000000\t38440000\t+\tSUPER_1\t2'..b'7\t21301\t10000\t20000\t-\tScaffold_5256\t89858\t33087\t43087\t4\t10000\t13\tid:f:0.950475\tkc:f:0.124528\n-Scaffold_4488\t21154\t0\t10000\t+\tScaffold_866\t87459\t26122\t36122\t11\t10000\t18\tid:f:0.983809\tkc:f:0.198607\n-Scaffold_4488\t21154\t10000\t20000\t+\tScaffold_866\t87459\t25607\t35607\t8\t10000\t16\tid:f:0.976785\tkc:f:0.148537\n-Scaffold_4489\t21062\t0\t10000\t-\tScaffold_670\t107290\t84863\t94863\t4\t10000\t13\tid:f:0.94815\tkc:f:0.282652\n-Scaffold_4490\t21043\t0\t21043\t-\tScaffold_6571\t37441\t16037\t37440\t13\t21879\t19\tid:f:0.987118\tkc:f:0.182177\n-Scaffold_4493\t20692\t0\t10000\t+\tScaffold_1025\t75996\t28426\t38426\t9\t10000\t17\tid:f:0.978886\tkc:f:0.168572\n-Scaffold_4494\t20661\t0\t20000\t+\tSUPER_1\t284047837\t198314978\t198335295\t18\t20317\t27\tid:f:0.997859\tkc:f:1.06245\n-Scaffold_4494\t20661\t10661\t20661\t+\tSUPER_1\t284047837\t198325987\t198335987\t19\t10000\t29\tid:f:0.998634\tkc:f:0.881866\n-Scaffold_4496\t20529\t0\t20000\t+\tScaffold_6441\t41434\t14093\t27028\t7\t20000\t16\tid:f:0.974415\tkc:f:0.242505\n-Scaffold_4496\t20529\t10529\t20529\t+\tScaffold_6441\t41434\t17028\t27028\t9\t10000\t17\tid:f:0.978886\tkc:f:0.18734\n-Scaffold_4497\t20477\t0\t10000\t+\tScaffold_1404\t54122\t16556\t26556\t7\t10000\t15\tid:f:0.967944\tkc:f:0.170893\n-Scaffold_4497\t20477\t10000\t20000\t+\tScaffold_772\t95721\t67677\t77677\t9\t10000\t16\tid:f:0.977014\tkc:f:0.246271\n-Scaffold_4499\t20196\t0\t20196\t+\tSUPER_13\t72503167\t66440184\t66460367\t20\t20196\t255\tid:f:1\tkc:f:1.04637\n-Scaffold_4499\t20196\t10000\t20000\t+\tSUPER_13\t72503167\t66450144\t66460144\t20\t10000\t255\tid:f:1\tkc:f:1.04413\n-Scaffold_4500\t20133\t0\t20133\t-\tScaffold_691\t103799\t56497\t73614\t12\t20133\t17\tid:f:0.980395\tkc:f:0.412303\n-Scaffold_4501\t20114\t0\t20114\t-\tSUPER_5\t199359660\t132061909\t132081562\t19\t20114\t255\tid:f:1\tkc:f:1.17327\n-Scaffold_4502\t20057\t0\t10000\t+\tScaffold_5810\t62207\t11308\t21308\t11\t10000\t19\tid:f:0.987387\tkc:f:0.107623\n-Scaffold_1916\t19923\t0\t19923\t-\tSUPER_16_unloc_5\t950142\t746919\t767071\t18\t20152\t31\tid:f:0.999279\tkc:f:1.08876\n-Scaffold_4504\t19853\t9853\t19853\t-\tScaffold_5519\t74355\t31179\t41179\t7\t10000\t16\tid:f:0.97203\tkc:f:0.155618\n-Scaffold_4505\t19644\t0\t10000\t+\tScaffold_881\t86338\t62404\t72404\t5\t10000\t13\tid:f:0.954968\tkc:f:0.34098\n-Scaffold_4507\t18958\t0\t18958\t+\tSUPER_12\t106695655\t8507943\t8526793\t19\t18958\t255\tid:f:1\tkc:f:0.687392\n-Scaffold_4508\t18891\t0\t10000\t+\tScaffold_6012\t54844\t44023\t54023\t5\t10000\t13\tid:f:0.954968\tkc:f:0.271754\n-Scaffold_4508\t18891\t8891\t18891\t+\tScaffold_5719\t65516\t48352\t58352\t5\t10000\t13\tid:f:0.954968\tkc:f:0.2781\n-Scaffold_4509\t18647\t0\t10000\t+\tSUPER_1\t284047837\t131702610\t131712610\t20\t10000\t255\tid:f:1\tkc:f:1.09836\n-Scaffold_1917\t18595\t0\t18595\t-\tScaffold_1534\t47765\t18847\t30756\t16\t18595\t22\tid:f:0.994102\tkc:f:0.209246\n-Scaffold_4511\t17841\t0\t17841\t+\tSUPER_3\t195712597\t40958532\t40976588\t20\t18056\t255\tid:f:1\tkc:f:0.860524\n-Scaffold_4512\t17529\t0\t17529\t-\tSUPER_7_unloc_2\t10283918\t7315881\t7333699\t20\t17818\t255\tid:f:1\tkc:f:1.10785\n-Scaffold_4513\t17242\t0\t17242\t+\tScaffold_39\t8708107\t2850560\t2867560\t20\t17242\t255\tid:f:1\tkc:f:1.01041\n-Scaffold_4514\t16816\t0\t10000\t-\tSUPER_7\t168114946\t98134412\t98144412\t20\t10000\t255\tid:f:1\tkc:f:0.892817\n-Scaffold_4515\t16179\t0\t16179\t+\tSUPER_1\t284047837\t191883496\t191899387\t20\t16179\t255\tid:f:1\tkc:f:1.14374\n-Scaffold_4516\t15810\t0\t10000\t-\tScaffold_484\t141143\t39859\t49859\t5\t10000\t14\tid:f:0.95711\tkc:f:0.173811\n-Scaffold_4516\t15810\t5810\t15810\t-\tScaffold_484\t141143\t39998\t49998\t5\t10000\t14\tid:f:0.95711\tkc:f:0.210937\n-Scaffold_4517\t13615\t0\t13615\t+\tScaffold_451\t151001\t55294\t68865\t18\t13615\t31\tid:f:0.999279\tkc:f:0.965465\n-Scaffold_4518\t11960\t0\t10000\t-\tScaffold_47\t5173787\t413309\t423309\t20\t10000\t255\tid:f:1\tkc:f:1.08847\n-Scaffold_4518\t11960\t1960\t11960\t-\tScaffold_47\t5173787\t411250\t421250\t19\t10000\t255\tid:f:1\tkc:f:0.951258\n-Scaffold_1918\t11724\t0\t10000\t+\tScaffold_38\t12621109\t9871182\t9881182\t20\t10000\t255\tid:f:1\tkc:f:1.33895\n-Scaffold_1918\t11724\t1724\t11724\t+\tScaffold_38\t12621109\t9872879\t9882879\t20\t10000\t255\tid:f:1\tkc:f:1.33895\n-Scaffold_4520\t10397\t0\t10000\t-\tScaffold_42\t5951611\t2859731\t2869731\t20\t10000\t255\tid:f:1\tkc:f:1.07975\n-Scaffold_4520\t10397\t397\t10397\t-\tScaffold_42\t5951611\t2859351\t2869351\t20\t10000\t255\tid:f:1\tkc:f:1.01323\n'

diff -r cec274db51c0 -r ed3a21033188 sortme.gff3
--- a/sortme.gff3 Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,15 +0,0 @@
-##gff-version 3
-###
-A01 Cufflinks mRNA 473 6154 . - . ID=XLOC_001154.41;description=Novel: Intergenic transcript
-A01 Cufflinks exon 473 814 . - . Parent=XLOC_001154.41
-A01 Cufflinks exon 1626 2574 . - . Parent=XLOC_001154.41
-A01 Cufflinks exon 2695 2721 . - . Parent=XLOC_001154.41
-A01 Cufflinks exon 3637 3726 . - . Parent=XLOC_001154.41
-A01 Cufflinks exon 5329 5408 . - . Parent=XLOC_001154.41
-A01 Cufflinks exon 5994 6154 . - . Parent=XLOC_001154.41
-###
-A01 Cufflinks mRNA 473 6386 . - . ID=XLOC_001154.42;description=Novel: Intergenic transcript
-A01 Cufflinks exon 473 2024 . - . Parent=XLOC_001154.42
-A01 Cufflinks exon 2615 2721 . - . Parent=XLOC_001154.42
-A01 Cufflinks exon 3637 3726 . - . Parent=XLOC_001154.42
-A01 Cufflinks exon 5329 6386 . - . Parent=XLOC_001154.42
\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 sout.gff
--- a/sout.gff Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,15 +0,0 @@
-A01 Cufflinks mRNA 473 6386 . - . ID=XLOC_001154.42;description=Novel: Intergenic transcript
-A01 Cufflinks mRNA 473 6154 . - . ID=XLOC_001154.41;description=Novel: Intergenic transcript
-A01 Cufflinks exon 5994 6154 . - . Parent=XLOC_001154.41
-A01 Cufflinks exon 5329 6386 . - . Parent=XLOC_001154.42
-A01 Cufflinks exon 5329 5408 . - . Parent=XLOC_001154.41
-A01 Cufflinks exon 473 814 . - . Parent=XLOC_001154.41
-A01 Cufflinks exon 473 2024 . - . Parent=XLOC_001154.42
-A01 Cufflinks exon 3637 3726 . - . Parent=XLOC_001154.42
-A01 Cufflinks exon 3637 3726 . - . Parent=XLOC_001154.41
-A01 Cufflinks exon 2695 2721 . - . Parent=XLOC_001154.41
-A01 Cufflinks exon 2615 2721 . - . Parent=XLOC_001154.42
-A01 Cufflinks exon 1626 2574 . - . Parent=XLOC_001154.41
-##gff-version 3
-###
-###
\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 squirrelhaps.paf
--- a/squirrelhaps.paf Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,26610 +0,0 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diff -r cec274db51c0 -r ed3a21033188 squirrelhaps1k.paf
--- a/squirrelhaps1k.paf Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,181217 +0,0 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diff -r cec274db51c0 -r ed3a21033188 test-data/gff3/sorted.gff
--- a/test-data/gff3/sorted.gff Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,558 +0,0 @@\n-##gff-version 3\n-##sequence-region Merlin 1 172788\n-Merlin\tannotation\tremark\t1\t172788\t.\t.\t.\tgff-version=3;sequence-region=%28%27Merlin%27%2C 0%2C 172788%29\n-Merlin\tfeature\tpolypeptide\t1\t229\t.\t+\t.\tID=Merlin_1;md5=4d58b2b569c2fe52e2945e3f6e380c48\n-Merlin\tGene3D\tprotein_match\t2\t50\t2.9E-21\t+\t.\tID=match%2477_2_50;Name=G3DSA:3.90.176.10;Target=Merlin_1 2 50;date=23-02-2015;status=T\n-Merlin\tSUPERFAMILY\tprotein_match\t2\t48\t.\t+\t.\tID=match%2479_2_48;Name=SSF56399;Target=Merlin_1 2 48;date=23-02-2015;status=T\n-Merlin\tPfam\tprotein_match\t7\t162\t1.9E-12\t+\t.\tDbxref=InterPro:IPR003540;ID=match%2478_7_162;Name=PF03496;Ontology_term=GO:0005576%22%2C%22GO:0009405;Target=Merlin_1 7 162;date=23-02-2015;signature_desc=ADP-ribosyltransferase exoenzyme;status=T\n-Merlin\tSUPERFAMILY\tprotein_match\t104\t164\t.\t+\t.\tID=match%2479_104_164;Name=SSF56399;Target=Merlin_1 104 164;date=23-02-2015;status=T\n-Merlin\tGene3D\tprotein_match\t106\t165\t2.9E-21\t+\t.\tID=match%2477_106_165;Name=G3DSA:3.90.176.10;Target=Merlin_1 106 165;date=23-02-2015;status=T\n-Merlin\tfeature\tpolypeptide\t1698\t2011\t.\t-\t.\tID=Merlin_3;md5=6b220b99a5d2dd40f55bb664a8dbdfb3\n-Merlin\tPfam\tprotein_match\t1912\t2011\t1.5E-8\t-\t.\tDbxref=InterPro:IPR010667;ID=match%24113_149_248;Name=PF06841;Ontology_term=GO:0005198;Target=Merlin_3 149 248;date=23-02-2015;signature_desc=T4-like virus tail tube protein gp19;status=T\n-Merlin\tfeature\tpolypeptide\t2716\t3066\t.\t-\t.\tID=Merlin_4;md5=bdb226d471fe35e28ce6a9ed4649a1f8\n-Merlin\tPfam\tprotein_match\t2725\t3066\t1.6E-150\t-\t.\tDbxref=InterPro:IPR024389;ID=match%24361_4_345;Name=PF11091;Target=Merlin_4 4 345;date=23-02-2015;signature_desc=Tail-tube assembly protein;status=T\n-Merlin\tfeature\tpolypeptide\t5144\t5317\t.\t-\t.\tID=Merlin_6;md5=c61e0e2dba259054b9c93fd931056fdd\n-Merlin\tPfam\tprotein_match\t5166\t5317\t1.5E-59\t-\t.\tDbxref=InterPro:IPR024342;ID=match%24360_21_172;Name=PF11110;Target=Merlin_6 21 172;date=23-02-2015;signature_desc=Baseplate hub distal subunit;status=T\n-Merlin\tfeature\tpolypeptide\t6052\t6431\t.\t-\t.\tID=Merlin_7;md5=b51a60ffef9f07b672e0d12d26d27bbc\n-Merlin\tPfam\tprotein_match\t6237\t6431\t4.3E-96\t-\t.\tDbxref=InterPro:IPR015181;ID=match%24229_4_198;Name=PF09097;Target=Merlin_7 4 198;date=23-02-2015;signature_desc=Baseplate structural protein,domain 1;status=T\n-Merlin\tSUPERFAMILY\tprotein_match\t6238\t6431\t.\t-\t.\tID=match%24228_5_198;Name=SSF69279;Target=Merlin_7 5 198;date=23-02-2015;status=T\n-Merlin\tSUPERFAMILY\tprotein_match\t6256\t6431\t.\t-\t.\tID=match%24227_199_374;Name=SSF69279;Target=Merlin_7 199 374;date=23-02-2015;status=T\n-Merlin\tPfam\tprotein_match\t6263\t6431\t3.9E-83\t-\t.\tDbxref=InterPro:IPR015180;ID=match%24231_201_369;Name=PF09096;Target=Merlin_7 201 369;date=23-02-2015;signature_desc=Baseplate structural protein,domain 2;status=T\n-Merlin\tGene3D\tprotein_match\t6320\t6431\t1.4E-54\t-\t.\tID=match%24230_3_114;Name=G3DSA:2.40.10.10;Target=Merlin_7 3 114;date=23-02-2015;status=T\n-Merlin\tfeature\tpolypeptide\t6931\t7180\t.\t-\t.\tID=Merlin_8;md5=78306f53371e5e47b051cad8a16b86e5\n-Merlin\tPfam\tprotein_match\t6985\t7180\t9.8E-56\t-\t.\tDbxref=InterPro:IPR024364;ID=match%24348_5_200;Name=PF12322;Target=Merlin_8 5 200;date=23-02-2015;signature_desc=T4 bacteriophage base plate protein;status=T\n-Merlin\tfeature\tpolypeptide\t7227\t7435\t.\t+\t.\tID=Merlin_9;md5=5ced4f78a57bd34e165ccf7b43ed3ef1\n-Merlin\tPfam\tprotein_match\t7231\t7433\t6.3E-63\t+\t.\tDbxref=InterPro:IPR024364;ID=match%24164_5_207;Name=PF12322;Target=Merlin_9 5 207;date=23-02-2015;signature_desc=T4 bacteriophage base plate protein;status=T\n-Merlin\tfeature\tpolypeptide\t7856\t7970\t.\t+\t.\tID=Merlin_10;md5=b0c491c633f373b9340ede7359636469\n-Merlin\tGene3D\tprotein_match\t7857\t7959\t9.3E-27\t+\t.\tDbxref=InterPro:IPR015801;ID=match%2418_2_104;Name=G3DSA:3.10.450.40;Ontology_term=GO:0005507%22%2C%22GO:0009308%22%2C%22GO:0048038;Target=Merlin_10 2 104;date=23-02-2015;status=T\n-Merlin\tSUPERFAMILY\tprotein_match\t7862\t7957\t.\t+\t.\tID=match%2417_7_102;Name=SSF160719;Target=Merlin_10 7 102;date=23-02-2015;status=T\n-Merlin\tPfam\tprotein_match\t7863\t7956\t1.6E-17\t+\t.\tDbxref=Inte'..b'0.1000;Target=Merlin_302 9 21;date=23-02-2015;status=T\n-Merlin\tPfam\tprotein_match\t166361\t166518\t6.6E-5\t+\t.\tDbxref=InterPro:IPR023214;ID=match%24166_11_168;Name=PF13419;Target=Merlin_302 11 168;date=23-02-2015;signature_desc=Haloacid dehalogenase-like hydrolase;status=T\n-Merlin\tGene3D\tprotein_match\t166428\t166561\t5.5E-6\t+\t.\tDbxref=InterPro:IPR023214;ID=match%24168_78_211;Name=G3DSA:3.40.50.1000;Target=Merlin_302 78 211;date=23-02-2015;status=T\n-Merlin\tfeature\tpolypeptide\t167486\t167970\t.\t+\t.\tID=Merlin_304;md5=283a418fea20ac001bffdcbf72299ca8\n-Merlin\tSUPERFAMILY\tprotein_match\t167619\t167850\t.\t+\t.\tID=match%24122_134_365;Name=SSF56091;Target=Merlin_304 134 365;date=23-02-2015;status=T\n-Merlin\tPfam\tprotein_match\t167620\t167850\t9.0E-28\t+\t.\tDbxref=InterPro:IPR012310%22%2C%22Reactome:REACT_216;ID=match%24125_135_365;Name=PF01068;Ontology_term=GO:0003910%22%2C%22GO:0005524%22%2C%22GO:0006281%22%2C%22GO:0006310;Target=Merlin_304 135 365;date=23-02-2015;signature_desc=ATP dependent DNA ligase domain;status=T\n-Merlin\tGene3D\tprotein_match\t167621\t167646\t8.5E-8\t+\t.\tID=match%24127_136_161;Name=G3DSA:3.30.1490.70;Target=Merlin_304 136 161;date=23-02-2015;status=T\n-Merlin\tProSitePatterns\tprotein_match\t167642\t167650\t.\t+\t.\tDbxref=InterPro:IPR016059%22%2C%22Reactome:REACT_216;ID=match%24126_157_165;Name=PS00697;Ontology_term=GO:0003909%22%2C%22GO:0051103;Target=Merlin_304 157 165;date=23-02-2015;signature_desc=ATP-dependent DNA ligase AMP-binding site.;status=T\n-Merlin\tGene3D\tprotein_match\t167661\t167794\t1.2E-4\t+\t.\tID=match%24129_176_309;Name=G3DSA:3.30.470.30;Target=Merlin_304 176 309;date=23-02-2015;status=T\n-Merlin\tGene3D\tprotein_match\t167803\t167833\t8.5E-8\t+\t.\tID=match%24127_318_348;Name=G3DSA:3.30.1490.70;Target=Merlin_304 318 348;date=23-02-2015;status=T\n-Merlin\tSUPERFAMILY\tprotein_match\t167823\t167930\t.\t+\t.\tDbxref=InterPro:IPR012340;ID=match%24128_338_445;Name=SSF50249;Target=Merlin_304 338 445;date=23-02-2015;status=T\n-Merlin\tProSitePatterns\tprotein_match\t167827\t167850\t.\t+\t.\tDbxref=InterPro:IPR016059%22%2C%22Reactome:REACT_216;ID=match%24124_342_365;Name=PS00333;Ontology_term=GO:0003909%22%2C%22GO:0051103;Target=Merlin_304 342 365;date=23-02-2015;signature_desc=ATP-dependent DNA ligase signature 2.;status=T\n-Merlin\tGene3D\tprotein_match\t167834\t167952\t5.9E-8\t+\t.\tDbxref=InterPro:IPR012340;ID=match%24123_349_467;Name=G3DSA:2.40.50.140;Target=Merlin_304 349 467;date=23-02-2015;status=T\n-Merlin\tfeature\tpolypeptide\t169174\t169869\t.\t+\t.\tID=Merlin_306;md5=3f61e1cb18fb135a3dc061968bcd879c\n-Merlin\tPfam\tprotein_match\t169589\t169781\t1.6E-22\t+\t.\tDbxref=InterPro:IPR003540;ID=match%24254_416_608;Name=PF03496;Ontology_term=GO:0005576%22%2C%22GO:0009405;Target=Merlin_306 416 608;date=23-02-2015;signature_desc=ADP-ribosyltransferase exoenzyme;status=T\n-Merlin\tSUPERFAMILY\tprotein_match\t169590\t169696\t.\t+\t.\tID=match%24253_417_523;Name=SSF56399;Target=Merlin_306 417 523;date=23-02-2015;status=T\n-Merlin\tGene3D\tprotein_match\t169597\t169698\t2.1E-28\t+\t.\tID=match%24255_424_525;Name=G3DSA:3.90.176.10;Target=Merlin_306 424 525;date=23-02-2015;status=T\n-Merlin\tSUPERFAMILY\tprotein_match\t169736\t169781\t.\t+\t.\tID=match%24253_563_608;Name=SSF56399;Target=Merlin_306 563 608;date=23-02-2015;status=T\n-Merlin\tGene3D\tprotein_match\t169738\t169784\t2.1E-28\t+\t.\tID=match%24255_565_611;Name=G3DSA:3.90.176.10;Target=Merlin_306 565 611;date=23-02-2015;status=T\n-Merlin\tfeature\tpolypeptide\t171300\t171794\t.\t+\t.\tID=Merlin_307;md5=0f4b8b0843334ccf18e5a4a7cbdf67b2\n-Merlin\tGene3D\tprotein_match\t171722\t171791\t5.2E-11\t+\t.\tID=match%24340_423_492;Name=G3DSA:3.90.176.10;Target=Merlin_307 423 492;date=23-02-2015;status=T\n-Merlin\tPfam\tprotein_match\t171723\t171791\t2.0E-9\t+\t.\tDbxref=InterPro:IPR003540;ID=match%24341_424_492;Name=PF03496;Ontology_term=GO:0005576%22%2C%22GO:0009405;Target=Merlin_307 424 492;date=23-02-2015;signature_desc=ADP-ribosyltransferase exoenzyme;status=T\n-Merlin\tSUPERFAMILY\tprotein_match\t171723\t171792\t.\t+\t.\tID=match%24339_424_493;Name=SSF56399;Target=Merlin_307 424 493;date=23-02-2015;status=T\n'

diff -r cec274db51c0 -r ed3a21033188 test-data/gff3/test.sh
--- a/test-data/gff3/test.sh Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-jbrowse sort-gff interpro.gff > sorted.gff

diff -r cec274db51c0 -r ed3a21033188 test-data/vcf/merlin.vcf.2
--- a/test-data/vcf/merlin.vcf.2 Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,23 +0,0 @@
-##fileformat=VCFv4.0
-##fileDate=20090805
-##source=myImputationProgramV3.1
-##reference=1000GenomesPilot-NCBI36
-##phasing=partial
-##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
-##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
-##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
-##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
-##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
-##FILTER=<ID=q10,Description="Quality below 10">
-##FILTER=<ID=s50,Description="Less than 50% of samples have data">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
-#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
-Merlin 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.
-Merlin 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3
-Merlin 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4
-Merlin 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2
-Merlin 1234567 microsat1 GTCT G,GTACT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3

diff -r cec274db51c0 -r ed3a21033188 test-data/vcf/merlinold.vcf
--- a/test-data/vcf/merlinold.vcf Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,23 +0,0 @@
-##fileformat=VCFv4.0
-##fileDate=20090805
-##source=myImputationProgramV3.1
-##reference=1000GenomesPilot-NCBI36
-##phasing=partial
-##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
-##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
-##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
-##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
-##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
-##FILTER=<ID=q10,Description="Quality below 10">
-##FILTER=<ID=s50,Description="Less than 50% of samples have data">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
-#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
-Merlin 61 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.
-Merlin 122 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3
-Merlin 488 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4
-Merlin 549 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2
-Merlin 1098 microsat1 G,GTACT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3

diff -r cec274db51c0 -r ed3a21033188 test.bed
--- a/test.bed Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,4006 +0,0 @@\n-SUPER_1 14830000 14840000 SUPER_1~14830000 2\n-SUPER_1 55680000 55690000 SUPER_1~55680000 2\n-SUPER_1 55690000 55690000 SUPER_1~55690000 4\n-SUPER_1 55710000 55710000 SUPER_1~55710000 3\n-SUPER_1 55720000 55720000 SUPER_1~55720000 4\n-SUPER_1 83690000 83700000 SUPER_1~83690000 6\n-SUPER_1 107760000 107780000 SUPER_1~107760000 2\n-SUPER_1 107800000 107840000 SUPER_1~107800000 3\n-SUPER_1 107810000 107830000 SUPER_1~107810000 2\n-SUPER_1 108170000 108200000 SUPER_1~108170000 2\n-SUPER_1 117460000 117480000 SUPER_1~117460000 2\n-SUPER_1 117550000 117550000 SUPER_1~117550000 3\n-SUPER_1 117560000 117560000 SUPER_1~117560000 3\n-SUPER_1 123740000 124980000 SUPER_1~123740000 2\n-SUPER_1 129250000 129350000 SUPER_1~129250000 2\n-SUPER_1 160420000 160430000 SUPER_1~160420000 2\n-SUPER_1 160430000 160440000 SUPER_1~160430000 3\n-SUPER_1 160770000 160780000 SUPER_1~160770000 2\n-SUPER_1 160810000 160820000 SUPER_1~160810000 2\n-SUPER_1 163330000 163350000 SUPER_1~163330000 2\n-SUPER_1 167310000 167330000 SUPER_1~167310000 2\n-SUPER_1 167930000 167950000 SUPER_1~167930000 2\n-SUPER_1 168170000 168170000 SUPER_1~168170000 3\n-SUPER_1 168400000 168420000 SUPER_1~168400000 2\n-SUPER_1 168440000 168490000 SUPER_1~168440000 2\n-SUPER_1 169780000 169790000 SUPER_1~169780000 2\n-SUPER_1 170210000 170240000 SUPER_1~170210000 2\n-SUPER_1 170260000 170280000 SUPER_1~170260000 2\n-SUPER_1 170320000 170330000 SUPER_1~170320000 2\n-SUPER_1 170450000 170470000 SUPER_1~170450000 3\n-SUPER_1 170580000 170600000 SUPER_1~170580000 2\n-SUPER_1 170670000 170670000 SUPER_1~170670000 3\n-SUPER_1 171410000 171420000 SUPER_1~171410000 2\n-SUPER_1 171450000 171460000 SUPER_1~171450000 2\n-SUPER_1 171470000 171480000 SUPER_1~171470000 2\n-SUPER_1 171490000 171500000 SUPER_1~171490000 5\n-SUPER_1 171770000 171780000 SUPER_1~171770000 2\n-SUPER_1 171860000 171870000 SUPER_1~171860000 2\n-SUPER_1 173040000 173050000 SUPER_1~173040000 2\n-SUPER_1 180600000 180610000 SUPER_1~180600000 4\n-SUPER_1 180880000 180880000 SUPER_1~180880000 3\n-SUPER_1 209520000 209530000 SUPER_1~209520000 3\n-SUPER_1 210120000 210130000 SUPER_1~210120000 2\n-SUPER_1 210620000 210630000 SUPER_1~210620000 3\n-SUPER_1 229580000 229590000 SUPER_1~229580000 3\n-SUPER_1 246120000 246130000 SUPER_1~246120000 2\n-SUPER_2 27960000 27970000 SUPER_2~27960000 8\n-SUPER_2 33100000 33120000 SUPER_2~33100000 2\n-SUPER_2 35480000 36050000 SUPER_2~35480000 2\n-SUPER_2 35490000 35510000 SUPER_2~35490000 2\n-SUPER_2 45800000 45820000 SUPER_2~45800000 2\n-SUPER_2 46280000 46290000 SUPER_2~46280000 9\n-SUPER_2 53560000 53570000 SUPER_2~53560000 8\n-SUPER_2 57350000 57360000 SUPER_2~57350000 8\n-SUPER_2 78720000 78720000 SUPER_2~78720000 3\n-SUPER_2 85460000 85460000 SUPER_2~85460000 3\n-SUPER_2 85490000 85490000 SUPER_2~85490000 3\n-SUPER_2 85600000 85600000 SUPER_2~85600000 3\n-SUPER_2 86420000 86420000 SUPER_2~86420000 3\n-SUPER_2 86440000 86440000 SUPER_2~86440000 3\n-SUPER_2 95170000 95180000 SUPER_2~95170000 3\n-SUPER_2 117270000 117280000 SUPER_2~117270000 2\n-SUPER_2 121570000 121580000 SUPER_2~121570000 2\n-SUPER_2 132510000 132520000 SUPER_2~132510000 2\n-SUPER_2 143490000 143500000 SUPER_2~143490000 2\n-SUPER_2 143670000 143680000 SUPER_2~143670000 10\n-SUPER_2 1544'..b'Scaffold_4303 18965 28965 Scaffold_4303~18965 2\n-Scaffold_4313 0 28765 Scaffold_4313~0 2\n-Scaffold_4320 0 10000 Scaffold_4320~0 12\n-Scaffold_4325 0 10000 Scaffold_4325~0 3\n-Scaffold_4337 10000 20000 Scaffold_4337~10000 2\n-Scaffold_4338 18143 28143 Scaffold_4338~18143 2\n-Scaffold_4339 0 10000 Scaffold_4339~0 4\n-Scaffold_4339 18125 28125 Scaffold_4339~18125 2\n-Scaffold_4347 0 0 Scaffold_4347~0 3\n-Scaffold_4352 0 10000 Scaffold_4352~0 2\n-Scaffold_4353 10000 20000 Scaffold_4353~10000 3\n-Scaffold_4354 0 20000 Scaffold_4354~0 5\n-Scaffold_4354 10000 27680 Scaffold_4354~10000 3\n-Scaffold_1885 0 10000 Scaffold_1885~0 5\n-Scaffold_1885 17678 27678 Scaffold_1885~17678 4\n-Scaffold_4363 0 27527 Scaffold_4363~0 3\n-Scaffold_4363 10000 27527 Scaffold_4363~10000 2\n-Scaffold_4364 0 10000 Scaffold_4364~0 6\n-Scaffold_4369 10000 20000 Scaffold_4369~10000 4\n-Scaffold_4370 0 10000 Scaffold_4370~0 4\n-Scaffold_4377 17025 27025 Scaffold_4377~17025 3\n-Scaffold_4381 0 20000 Scaffold_4381~0 3\n-Scaffold_4383 10000 20000 Scaffold_4383~10000 2\n-Scaffold_1893 16557 26557 Scaffold_1893~16557 3\n-Scaffold_4392 0 10000 Scaffold_4392~0 2\n-Scaffold_4394 0 10000 Scaffold_4394~0 2\n-Scaffold_4398 16315 26315 Scaffold_4398~16315 6\n-Scaffold_4401 0 10000 Scaffold_4401~0 2\n-Scaffold_4402 0 0 Scaffold_4402~0 3\n-Scaffold_1897 0 10000 Scaffold_1897~0 2\n-Scaffold_1897 15997 25997 Scaffold_1897~15997 3\n-Scaffold_4409 15953 25953 Scaffold_4409~15953 2\n-Scaffold_4410 0 10000 Scaffold_4410~0 3\n-Scaffold_1900 10000 20000 Scaffold_1900~10000 2\n-Scaffold_4423 15334 25334 Scaffold_4423~15334 2\n-Scaffold_4430 14940 24940 Scaffold_4430~14940 3\n-Scaffold_4439 10000 20000 Scaffold_4439~10000 2\n-Scaffold_4440 0 10000 Scaffold_4440~0 15\n-Scaffold_4440 10000 20000 Scaffold_4440~10000 2\n-Scaffold_4449 10000 20000 Scaffold_4449~10000 2\n-Scaffold_4451 13691 23691 Scaffold_4451~13691 2\n-Scaffold_4456 10000 23421 Scaffold_4456~10000 4\n-Scaffold_4458 10000 20000 Scaffold_4458~10000 3\n-Scaffold_4458 13383 23383 Scaffold_4458~13383 4\n-Scaffold_4459 0 10000 Scaffold_4459~0 2\n-Scaffold_4459 13381 23381 Scaffold_4459~13381 2\n-Scaffold_4460 10000 20000 Scaffold_4460~10000 3\n-Scaffold_1910 0 0 Scaffold_1910~0 3\n-Scaffold_4465 10000 20000 Scaffold_4465~10000 2\n-Scaffold_4468 10000 20000 Scaffold_4468~10000 3\n-Scaffold_4470 10000 20000 Scaffold_4470~10000 3\n-Scaffold_4470 12694 22694 Scaffold_4470~12694 4\n-Scaffold_4471 0 10000 Scaffold_4471~0 7\n-Scaffold_4474 0 10000 Scaffold_4474~0 3\n-Scaffold_4475 10000 20000 Scaffold_4475~10000 5\n-Scaffold_4485 0 21311 Scaffold_4485~0 5\n-Scaffold_4485 10000 20000 Scaffold_4485~10000 4\n-Scaffold_4485 11311 21311 Scaffold_4485~11311 2\n-Scaffold_4486 0 10000 Scaffold_4486~0 3\n-Scaffold_4489 0 10000 Scaffold_4489~0 2\n-Scaffold_4508 8891 18891 Scaffold_4508~8891 2\n-Scaffold_4512 0 10000 Scaffold_4512~0 2\n-Scaffold_4516 0 10000 Scaffold_4516~0 4\n-Scaffold_4516 5810 15810 Scaffold_4516~5810 3\n-Scaffold_4518 0 10000 Scaffold_4518~0 7\n-Scaffold_4518 1960 11960 Scaffold_4518~1960 7\n-Scaffold_1918 0 10000 Scaffold_1918~0 3\n-Scaffold_1918 1724 11724 Scaffold_1918~1724 4\n-Scaffold_4520 0 10000 Scaffold_4520~0 2\n-Scaffold_4520 397 10397 Scaffold_4520~397 2\n'

diff -r cec274db51c0 -r ed3a21033188 test1k.bed
--- a/test1k.bed Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,24124 +0,0 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diff -r cec274db51c0 -r ed3a21033188 x/Merlin.fa.gz

Binary file x/Merlin.fa.gz has changed

diff -r cec274db51c0 -r ed3a21033188 x/Merlin.fa.gz.fai
--- a/x/Merlin.fa.gz.fai Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-Merlin 172788 8 60 61

diff -r cec274db51c0 -r ed3a21033188 x/Merlin.fa.gz.gzi

Binary file x/Merlin.fa.gz.gzi has changed

diff -r cec274db51c0 -r ed3a21033188 x/Ppersica1.fa.fa.gz

Binary file x/Ppersica1.fa.fa.gz has changed

diff -r cec274db51c0 -r ed3a21033188 x/Ppersica1.fa.fa.gz.fai
--- a/x/Ppersica1.fa.fa.gz.fai Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-Pp01 47851208 6 80 81

diff -r cec274db51c0 -r ed3a21033188 x/Ppersica1.fa.fa.gz.gzi

Binary file x/Ppersica1.fa.fa.gz.gzi has changed

diff -r cec274db51c0 -r ed3a21033188 x/Vvinifera1.fa.fa.gz

Binary file x/Vvinifera1.fa.fa.gz has changed

diff -r cec274db51c0 -r ed3a21033188 x/Vvinifera1.fa.fa.gz.fai
--- a/x/Vvinifera1.fa.fa.gz.fai Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-chr1 23037639 6 60 61

diff -r cec274db51c0 -r ed3a21033188 x/Vvinifera1.fa.fa.gz.gzi

Binary file x/Vvinifera1.fa.fa.gz.gzi has changed

diff -r cec274db51c0 -r ed3a21033188 x/arabgrapepeach.paf_11
--- a/x/arabgrapepeach.paf_11 Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,129777 +0,0 @@\n-Pp01\t47851208\t35000\t36000\t-\tchrUn\t43154196\t26047489\t26048489\t2\t1000\t8\tid:f:0.831914\tkc:f:0.902879\n-Pp01\t47851208\t38000\t39000\t+\tchr5\t25021643\t13537\t14537\t2\t1000\t8\tid:f:0.831914\tkc:f:0.93693\n-Pp01\t47851208\t39000\t40000\t+\tchr17\t17126926\t909039\t910039\t2\t1000\t8\tid:f:0.831914\tkc:f:1.02305\n-Pp01\t47851208\t45000\t46000\t-\tchr8\t22385789\t8160875\t8161875\t3\t1000\t8\tid:f:0.849858\tkc:f:0.913698\n-Pp01\t47851208\t49000\t50000\t-\tchr8\t22385789\t8155127\t8156127\t3\t1000\t8\tid:f:0.84952\tkc:f:0.957541\n-Pp01\t47851208\t50000\t51000\t-\tchr4\t23867706\t20888907\t20889907\t2\t1000\t8\tid:f:0.831914\tkc:f:0.976315\n-Pp01\t47851208\t51000\t52000\t-\tchrUn\t43154196\t5300440\t5301440\t2\t1000\t8\tid:f:0.831914\tkc:f:0.940799\n-Pp01\t47851208\t52000\t53000\t+\tchr17\t17126926\t9200962\t9201962\t1\t1000\t7\tid:f:0.803743\tkc:f:0.94545\n-Pp01\t47851208\t57000\t58000\t-\tchr9\t23006712\t19917499\t19918499\t2\t1000\t8\tid:f:0.831914\tkc:f:0.936352\n-Pp01\t47851208\t61000\t62000\t+\tchr7_random\t1447032\t361032\t362032\t2\t1000\t8\tid:f:0.832921\tkc:f:1.05875\n-Pp01\t47851208\t63000\t64000\t-\tchr6\t21508407\t19577351\t19578351\t2\t1000\t8\tid:f:0.831914\tkc:f:1.11331\n-Pp01\t47851208\t65000\t66000\t+\tchr17\t17126926\t15161009\t15162009\t2\t1000\t8\tid:f:0.832247\tkc:f:0.975446\n-Pp01\t47851208\t68000\t69000\t-\tchr8\t22385789\t13787780\t13788780\t2\t1000\t8\tid:f:0.831914\tkc:f:0.922845\n-Pp01\t47851208\t70000\t71000\t-\tchr10\t18140952\t976100\t977100\t1\t1000\t7\tid:f:0.803082\tkc:f:1.04989\n-Pp01\t47851208\t70000\t71000\t-\tchr11\t19818926\t37304\t38304\t1\t1000\t7\tid:f:0.803082\tkc:f:1.04989\n-Pp01\t47851208\t70000\t71000\t+\tchr12_random\t1566225\t1092287\t1093287\t1\t1000\t7\tid:f:0.803082\tkc:f:1.04989\n-Pp01\t47851208\t70000\t71000\t+\tchr13\t24396255\t918733\t919733\t1\t1000\t7\tid:f:0.803082\tkc:f:1.04989\n-Pp01\t47851208\t70000\t71000\t-\tchr13_random\t3268264\t493723\t494723\t1\t1000\t7\tid:f:0.803082\tkc:f:1.04989\n-Pp01\t47851208\t70000\t71000\t+\tchr14\t30274277\t14893114\t14894114\t1\t1000\t7\tid:f:0.803082\tkc:f:1.04989\n-Pp01\t47851208\t70000\t71000\t-\tchr15\t20304914\t5219516\t5220516\t1\t1000\t7\tid:f:0.803082\tkc:f:1.04989\n-Pp01\t47851208\t70000\t71000\t+\tchr18\t29360087\t6814496\t6815496\t1\t1000\t7\tid:f:0.803082\tkc:f:1.04989\n-Pp01\t47851208\t70000\t71000\t-\tchr18_random\t5170003\t2374998\t2375998\t1\t1000\t7\tid:f:0.803082\tkc:f:1.04989\n-Pp01\t47851208\t70000\t71000\t+\tchr2\t18779844\t13142265\t13143265\t1\t1000\t7\tid:f:0.803082\tkc:f:1.04989\n-Pp01\t47851208\t70000\t71000\t+\tchr4\t23867706\t4401454\t4402454\t1\t1000\t7\tid:f:0.803082\tkc:f:1.04989\n-Pp01\t47851208\t70000\t71000\t+\tchr5\t25021643\t9615855\t9616855\t1\t1000\t7\tid:f:0.803082\tkc:f:1.04989\n-Pp01\t47851208\t70000\t71000\t-\tchr6\t21508407\t6605517\t6606517\t1\t1000\t7\tid:f:0.803082\tkc:f:1.04989\n-Pp01\t47851208\t70000\t71000\t-\tchr7\t21026613\t13058043\t13059043\t1\t1000\t7\tid:f:0.803082\tkc:f:1.04989\n-Pp01\t47851208\t70000\t71000\t-\tchr8\t22385789\t3728038\t3729038\t1\t1000\t7\tid:f:0.803082\tkc:f:1.04989\n-Pp01\t47851208\t70000\t71000\t+\tchr9\t23006712\t52405\t53405\t1\t1000\t7\tid:f:0.803082\tkc:f:1.04989\n-Pp01\t47851208\t70000\t71000\t-\tchrUn\t43154196\t13784146\t13785146\t1\t1000\t7\tid:f:0.803082\tkc:f:1.04989\n-Pp01\t47851208\t72000\t73000\t-\tchr9\t23006712\t13783681\t13784681\t2\t1000\t8\tid:f:0.831914\tkc:f:1.02185\n-Pp01\t47851208\t73000\t74000\t-\tchr9\t23006712\t13774329\t13775329\t2\t1000\t8\tid:f:0.831914\tkc:f:0.827802\n-Pp01\t47851208\t80000\t81000\t-\tchr9\t23006712\t13696163\t13697163\t2\t1000\t8\tid:f:0.831914\tkc:f:0.941547\n-Pp01\t47851208\t81000\t82000\t+\tENA|CP002687|CP002687.1\t18585056\t14039503\t14040503\t2\t1000\t8\tid:f:0.831914\tkc:f:1.09962\n-Pp01\t47851208\t96000\t97000\t-\tchr13\t24396255\t2677686\t2678686\t2\t1000\t8\tid:f:0.831914\tkc:f:1.05334\n-Pp01\t47851208\t97000\t98000\t-\tchr18\t29360087\t6935515\t6936515\t2\t1000\t8\tid:f:0.831914\tkc:f:0.970351\n-Pp01\t47851208\t99000\t100000\t-\tchr13\t24396255\t7211769\t7212769\t2\t1000\t8\tid:f:0.831914\tkc:f:1.0044\n-Pp01\t47851208\t111000\t112000\t-\tchr14\t30274277\t18152296\t18153296\t1\t1000\t7\tid:f:0.803411\tkc:f:0.878718\n-Pp01\t47851208\t111000\t112000\t+\tchr16\t22053297\t19812596\t19813596\t1\t1000\t7\tid:f:0.803411\tkc:f:0.878718\n-Pp01\t47851208\t111000\t112000\t-\tchrUn\t43154196\t21909280\t21910280\t1\t1000\t7\tid:f:0.803411\tkc:f:0.878718\n-Pp01\t47851208\t115000\t116000\t-\tENA|CP002684|CP002684.1\t30427671\t13495595\t13496595\t2'..b'3154196\t1391485\t1392485\t1\t1000\t7\tid:f:0.803082\tkc:f:0.948159\n-scaffold_191\t4575\t3575\t4575\t+\tENA|CP002684|CP002684.1\t30427671\t11730328\t11731328\t1\t1000\t7\tid:f:0.803082\tkc:f:0.948159\n-scaffold_191\t4575\t3575\t4575\t-\tENA|CP002685|CP002685.1\t19698289\t7583468\t7584468\t1\t1000\t7\tid:f:0.803082\tkc:f:0.948159\n-scaffold_191\t4575\t3575\t4575\t+\tENA|CP002686|CP002686.1\t23459830\t511225\t512225\t1\t1000\t7\tid:f:0.803082\tkc:f:0.948159\n-scaffold_191\t4575\t3575\t4575\t-\tENA|CP002687|CP002687.1\t18585056\t5706977\t5707977\t1\t1000\t7\tid:f:0.803082\tkc:f:0.948159\n-scaffold_191\t4575\t3575\t4575\t+\tENA|CP002688|CP002688.1\t26975502\t6027002\t6028002\t1\t1000\t7\tid:f:0.803082\tkc:f:0.948159\n-scaffold_247\t4525\t3000\t4000\t+\tchr18_random\t5170003\t4724786\t4725786\t2\t1000\t8\tid:f:0.831914\tkc:f:0.918526\n-scaffold_247\t4525\t3525\t4525\t+\tchr18_random\t5170003\t4724786\t4725786\t2\t1000\t8\tid:f:0.831914\tkc:f:0.841707\n-scaffold_220\t4478\t0\t1000\t-\tchr13\t24396255\t14240906\t14241906\t2\t1000\t8\tid:f:0.831914\tkc:f:0.691279\n-scaffold_220\t4478\t1000\t2000\t+\tchr17\t17126926\t15135135\t15136135\t2\t1000\t8\tid:f:0.831914\tkc:f:0.845202\n-scaffold_220\t4478\t2000\t3000\t+\tchr17\t17126926\t15135135\t15136135\t2\t1000\t8\tid:f:0.831914\tkc:f:0.592864\n-scaffold_220\t4478\t3000\t4000\t+\tchr17\t17126926\t15135135\t15136135\t2\t1000\t8\tid:f:0.831914\tkc:f:0.885933\n-scaffold_220\t4478\t3478\t4478\t+\tchr17\t17126926\t15135135\t15136135\t2\t1000\t8\tid:f:0.831914\tkc:f:0.851145\n-scaffold_231\t4391\t0\t1000\t+\tchr15\t20304914\t1778930\t1779930\t2\t1000\t8\tid:f:0.831914\tkc:f:0.984577\n-scaffold_231\t4391\t2000\t3000\t-\tchrUn\t43154196\t6514075\t6515075\t2\t1000\t8\tid:f:0.832247\tkc:f:0.530935\n-scaffold_231\t4391\t3391\t4391\t+\tchr15\t20304914\t1778930\t1779930\t2\t1000\t8\tid:f:0.831914\tkc:f:1.1372\n-scaffold_259\t3708\t0\t1000\t-\tchr17\t17126926\t1371257\t1372257\t1\t1000\t7\tid:f:0.804415\tkc:f:0.84608\n-scaffold_259\t3708\t2000\t3000\t-\tENA|CP002685|CP002685.1\t19698289\t558514\t559514\t2\t1000\t8\tid:f:0.831914\tkc:f:0.7915\n-scaffold_254\t3576\t0\t1000\t-\tchr18_random\t5170003\t4101235\t4102235\t2\t1000\t8\tid:f:0.831914\tkc:f:0.938495\n-scaffold_254\t3576\t1000\t2000\t-\tchr18_random\t5170003\t4101350\t4102350\t2\t1000\t8\tid:f:0.831914\tkc:f:0.784942\n-scaffold_254\t3576\t1000\t2000\t+\tchrUn\t43154196\t37819369\t37820369\t2\t1000\t8\tid:f:0.831914\tkc:f:0.784942\n-scaffold_254\t3576\t2576\t3576\t-\tchr18_random\t5170003\t4101359\t4102359\t2\t1000\t8\tid:f:0.831914\tkc:f:0.855605\n-scaffold_255\t3476\t0\t1000\t-\tchr18\t29360087\t22938806\t22939806\t2\t1000\t8\tid:f:0.833262\tkc:f:0.879877\n-scaffold_270\t3362\t0\t1000\t-\tchrUn\t43154196\t28843065\t28844065\t2\t1000\t8\tid:f:0.831914\tkc:f:1.08283\n-scaffold_270\t3362\t1000\t2000\t-\tchr18\t29360087\t11597680\t11598680\t2\t1000\t8\tid:f:0.831914\tkc:f:0.901259\n-scaffold_270\t3362\t2000\t3000\t+\tchr11\t19818926\t12454100\t12455100\t2\t1000\t8\tid:f:0.831914\tkc:f:0.831158\n-scaffold_270\t3362\t2362\t3362\t+\tchr11\t19818926\t12454100\t12455100\t2\t1000\t8\tid:f:0.831914\tkc:f:0.788287\n-scaffold_308\t2380\t0\t1000\t+\tchrUn\t43154196\t26022131\t26023131\t2\t1000\t8\tid:f:0.833262\tkc:f:0.814096\n-scaffold_308\t2380\t1000\t2000\t+\tchr6\t21508407\t7794186\t7795186\t2\t1000\t8\tid:f:0.833262\tkc:f:0.769516\n-scaffold_308\t2380\t1380\t2380\t+\tchr6\t21508407\t7794186\t7795186\t2\t1000\t8\tid:f:0.833262\tkc:f:0.850835\n-scaffold_333\t1452\t0\t1000\t+\tchr1\t23037639\t8089320\t8090320\t2\t1000\t8\tid:f:0.832247\tkc:f:1.0009\n-scaffold_333\t1452\t0\t1000\t+\tchr6\t21508407\t7794067\t7795067\t2\t1000\t8\tid:f:0.832247\tkc:f:1.0009\n-scaffold_333\t1452\t452\t1452\t+\tchr6\t21508407\t7794067\t7795067\t2\t1000\t8\tid:f:0.832582\tkc:f:0.850166\n-scaffold_338\t1306\t0\t1000\t+\tENA|CP002688|CP002688.1\t26975502\t1913479\t1914479\t3\t1000\t8\tid:f:0.84952\tkc:f:0.919077\n-scaffold_338\t1306\t306\t1306\t+\tENA|CP002688|CP002688.1\t26975502\t1913479\t1914479\t3\t1000\t8\tid:f:0.84952\tkc:f:0.917352\n-scaffold_344\t1163\t0\t1000\t+\tchr9\t23006712\t14055684\t14056684\t2\t1000\t8\tid:f:0.831914\tkc:f:1.08801\n-scaffold_344\t1163\t163\t1163\t+\tchr9\t23006712\t14055553\t14056553\t3\t1000\t8\tid:f:0.850198\tkc:f:1.04507\n-scaffold_349\t1099\t0\t1000\t-\tENA|CP002687|CP002687.1\t18585056\t11626986\t11627986\t2\t1000\t8\tid:f:0.831914\tkc:f:1.05856\n-scaffold_349\t1099\t99\t1099\t-\tENA|CP002687|CP002687.1\t18585056\t11626986\t11627986\t2\t1000\t8\tid:f:0.831914\tkc:f:1.06329\n'

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diff -r cec274db51c0 -r ed3a21033188 x/arabgrapepeach.paf_12
--- a/x/arabgrapepeach.paf_12 Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/bedscoreplugin.js
--- a/x/bedscoreplugin.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,26 +0,0 @@
-// colour bed regions according to score - must have columns and score as part of the adapter setup
-;(function () {
-  class Plugin {
-    name = 'BedScorePlugin';
-    version = '1.0';
-
-    install(pluginManager) {
-      pluginManager.jexl.addFunction('customColor', feature => {
-        if (Number(feature.get('score')) > 0) {
-          return 'red';
-        } else {
-          return 'blue';
-        }
-      })
-    }
-
-    configure(pluginManager) {}
-  }
-
-  // the plugin will be included in both the main thread and web worker, so
-  // install plugin to either window or self (webworker global scope)
-  ;(typeof self !== 'undefined' ? self : window).JBrowsePluginBedScorePlugin =
-    {
-      default: Plugin,
-    }
-})()

diff -r cec274db51c0 -r ed3a21033188 x/build_env_setup.sh
--- a/x/build_env_setup.sh Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,396 +0,0 @@\n-export CONDA_BUILD="1"\n-export PYTHONNOUSERSITE="1"\n-export CONDA_DEFAULT_ENV="/home/ross/miniconda3/envs/mulled-v1-ead19212d339c2197ed3232dcd8366627d23ccb1cf4fb8ae3186545effdca881"\n-export ARCH="64"\n-export PREFIX="/home/ross/miniconda3/envs/mulled-v1-ead19212d339c2197ed3232dcd8366627d23ccb1cf4fb8ae3186545effdca881"\n-export BUILD_PREFIX="/opt/conda/conda-bld/jbrowse2_1726856947541/_build_env"\n-export SYS_PREFIX="/opt/conda"\n-export SYS_PYTHON="/opt/conda/bin/python"\n-export SUBDIR="linux-64"\n-export build_platform="linux-64"\n-export SRC_DIR="/opt/conda/conda-bld/jbrowse2_1726856947541/work"\n-export ROOT="/opt/conda"\n-export CONDA_PY="312"\n-export PY3K="1"\n-export PY_VER="3.12"\n-export STDLIB_DIR="/home/ross/miniconda3/envs/mulled-v1-ead19212d339c2197ed3232dcd8366627d23ccb1cf4fb8ae3186545effdca881/lib/python3.12"\n-export SP_DIR="/home/ross/miniconda3/envs/mulled-v1-ead19212d339c2197ed3232dcd8366627d23ccb1cf4fb8ae3186545effdca881/lib/python3.12/site-packages"\n-export NPY_VER="1.26"\n-export CONDA_NPY="126"\n-export NPY_DISTUTILS_APPEND_FLAGS="1"\n-export PERL_VER="5.32"\n-export CONDA_PERL="5.32"\n-export LUA_VER="5"\n-export CONDA_LUA="5"\n-export R_VER="4.3.*"\n-export CONDA_R="4.3.*"\n-export PKG_NAME="jbrowse2"\n-export PKG_VERSION="2.15.4"\n-export PKG_BUILDNUM="0"\n-export PKG_BUILD_STRING="placeholder"\n-export PKG_HASH="1234567"\n-export RECIPE_DIR="/opt/recipe"\n-export CPU_COUNT="2"\n-export LANG="C.UTF-8"\n-export SHLIB_EXT=".so"\n-export PATH="/opt/conda/conda-bld/jbrowse2_1726856947541/_build_env/bin:/home/ross/miniconda3/envs/mulled-v1-ead19212d339c2197ed3232dcd8366627d23ccb1cf4fb8ae3186545effdca881/bin:/opt/conda/bin:/opt/conda/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/conda/bin"\n-export HOME="/home/conda"\n-export PKG_CONFIG_PATH="/home/ross/miniconda3/envs/mulled-v1-ead19212d339c2197ed3232dcd8366627d23ccb1cf4fb8ae3186545effdca881/lib/pkgconfig"\n-export CMAKE_GENERATOR="Unix Makefiles"\n-export LD_RUN_PATH="/home/ross/miniconda3/envs/mulled-v1-ead19212d339c2197ed3232dcd8366627d23ccb1cf4fb8ae3186545effdca881/lib"\n-export BUILD="x86_64-conda_cos6-linux-gnu"\n-export zip_keys="[[\'c_compiler_version\', \'cxx_compiler_version\', \'fortran_compiler_version\'], [\'arrow_cpp\', \'libarrow\', \'libarrow_all\'], [\'python\', \'numpy\', \'python_impl\'], [\'c_stdlib_version\', \'cdt_name\']]"\n-export pin_run_as_build="OrderedDict([(\'python\', {\'min_pin\': \'x.x\', \'max_pin\': \'x.x\'}), (\'r-base\', {\'max_pin\': \'x.x\', \'min_pin\': \'x.x\'}), (\'flann\', {\'max_pin\': \'x.x.x\'}), (\'graphviz\', {\'max_pin\': \'x\'}), (\'libsvm\', {\'max_pin\': \'x\'}), (\'netcdf-cxx4\', {\'max_pin\': \'x.x\'}), (\'occt\', {\'max_pin\': \'x.x\'}), (\'poppler\', {\'max_pin\': \'x.x\'}), (\'vlfeat\', {\'max_pin\': \'x.x.x\'})])"\n-export extend_keys="{\'ignore_version\', \'pin_run_as_build\', \'extend_keys\', \'ignore_build_only_deps\'}"\n-export ignore_build_only_deps="{\'python\', \'numpy\'}"\n-export libyarp="3.9.0"\n-export libintervalxt="3"\n-export tk="8.6"\n-export libmatio="1.5.26"\n-export qt="5.15"\n-export coin_or_cgl="0.60"\n-export coincbc="2.10"\n-export pixman="0"\n-export libhugetlbfs="2"\n-export libopencv="4.9.0"\n-export ccr="1.3"\n-export superlu_dist="8"\n-export libsoup="3"\n-export pyqtwebengine="5.15"\n-export hdf4="4.2.15"\n-export gst_plugins_base="1.22"\n-export eclib="20231211"\n-export google_cloud_cpp_common="0.25.0"\n-export dcap="2.47"\n-export slepc4py="3.21"\n-export scotch="7.0.4"\n-export snappy="1.2"\n-export suitesparse="5"\n-export libblitz="1.0.2"\n-export libabseil_static="20220623.0"\n-export libflatsurf="3"\n-export pulseaudio="17.0"\n-export libcblas="3.9 *netlib"\n-export libgoogle_cloud_dlp_devel="2.24"\n-export rocksdb="9.1"\n-export _libgcc_mutex="0.1 conda_forge"\n-export gnuradio_core="3.10.10"\n-export librdkafka="2.4"\n-export libdap4="3.20.6"\n-export aws_c_auth="0.7.22"\n-export channel_targets="bioconda main"\n-export libhwloc="2.10.0"\n-export pyqt="5.15"\n-export cpu_optimization_target="nocona"\n-export assimp="5.3.1"\n-export mpfr="4"\n-export pcre2="10.43"\n-export gsl="2.7"\n-expor'..b'h="2.1"\n-export pulseaudio_client="17.0"\n-export aws_crt_cpp="0.26.9"\n-export pango="1.50"\n-export alsa_lib="1.2"\n-export bzip2="1"\n-export tbb="2021"\n-export root_base="6.28.10"\n-export libnetcdf="4.9.2"\n-export cran_mirror="https://cran.r-project.org"\n-export wxwidgets="3.2"\n-export orc="2.0.1"\n-export singular="4.3.2.p8"\n-export libspatialindex="1.9.3"\n-export p11_kit="0.24"\n-export cuda_compiler="None"\n-export log4cxx="1.2.0"\n-export cuda_compiler_version_min="11.8"\n-export msgpack_cxx="6"\n-export libxml2="2"\n-export fftw="3"\n-export libuuid="2"\n-export wcslib="8"\n-export VERBOSE_AT="V=1"\n-export cudnn="8"\n-export mkl="2023"\n-export ldas_tools_framecpp="2.9"\n-export libgoogle_cloud_aiplatform_devel="2.24"\n-export pyqtchart="5.15"\n-export qtkeychain="0.14"\n-export blas_impl="blis"\n-export nss="3"\n-export gdk_pixbuf="2"\n-export gf2x="1.3"\n-export tensorflow="2.15"\n-export liblapacke="3.9 *netlib"\n-export libgoogle_cloud_spanner_devel="2.24"\n-export pcl="1.14.0"\n-export krb5="1.21"\n-export libsvm="332"\n-export libexactreal="4"\n-export cgo_compiler="go-cgo"\n-export petsc4py="3.21"\n-export poppler="24.04"\n-export aws_c_event_stream="0.4.2"\n-export vtk="9.2.6"\n-export libkml="1.3"\n-export libssh="0.10"\n-export flann="1.9.2"\n-export gfal2="2.22"\n-export cfitsio="4.3.0"\n-export s2n="1.4.15"\n-export rdma_core="51"\n-export json_c="0.17"\n-export zfp="1.0"\n-export libgoogle_cloud_devel="2.24"\n-export giflib="5.2"\n-export soapysdr="0.8"\n-export libblas="3.9 *netlib"\n-export openjpeg="2"\n-export mkl_devel="2023"\n-export imath="3.1.11"\n-export glib="2"\n-export libboost_devel="1.82"\n-export target_gobin="${PREFIX}/bin/"\n-export libsentencepiece="0.2.0"\n-export pugixml="1.14"\n-export antic="0.2"\n-export libgoogle_cloud_bigtable_devel="2.24"\n-export sdl2="2"\n-export ipopt="3.14.16"\n-export mumps_mpi="5.7.1"\n-export qt_main="5.15"\n-export c_ares="1"\n-export volk="3.1"\n-export libgoogle_cloud_pubsub_devel="2.24"\n-export aws_c_cal="0.6.14"\n-export ffmpeg="6"\n-export libunwind="1.6"\n-export gmp="6"\n-export sdl2_ttf="2"\n-export capnproto="1.0.2"\n-export isl="0.26"\n-export libgoogle_cloud_iam_devel="2.24"\n-export libaec="1"\n-export tbb_devel="2021"\n-export xerces_c="3.2"\n-export liblapack="3.9 *netlib"\n-export cairo="1"\n-export libtiff="4.6"\n-export aws_c_io="0.14.8"\n-export dav1d="1.2.1"\n-export lerc="4"\n-export target_goarch="amd64"\n-export proj="9.3.1"\n-export arb="2.23"\n-export aws_c_mqtt="0.10.4"\n-export libgoogle_cloud_speech_devel="2.24"\n-export expat="2"\n-export bullet_cpp="3.25"\n-export srm_ifce="1.24.6"\n-export libgoogle_cloud_storage_devel="2.24"\n-export libavif="1"\n-export postgresql="16"\n-export glpk="5.0"\n-export graphviz="9"\n-export lmdb="0.9.29"\n-export flatbuffers="24.3.25"\n-export libxsmm="1"\n-export freetype="2"\n-export console_bridge="1.0"\n-export libgoogle_cloud="2.24"\n-export aom="3.8"\n-export rust_compiler="rust"\n-export libgoogle_cloud_all_devel="2.24"\n-export libdeflate="1.20"\n-export nccl="2"\n-export libgoogle_cloud_discoveryengine_devel="2.24"\n-export attr="2.5"\n-export gsoap="2.8.123"\n-export starlink_ast="9.2.7"\n-export fortran_compiler="gfortran"\n-export r_base="4.3.*"\n-export libwebp="1"\n-export libsndfile="1.2"\n-export poco="1.13.3"\n-export libosqp="0.6.3"\n-export arrow_cpp="15"\n-export libarrow="15"\n-export libarrow_all="15"\n-export python_impl="cpython"\n-export c_stdlib_version="2.17"\n-export cdt_name="cos6"\n-export c_compiler_version="12"\n-export cxx_compiler_version="12"\n-export fortran_compiler_version="12"\n-export CONDA_BUILD_STATE="BUILD"\n-export PIP_NO_BUILD_ISOLATION="False"\n-export PIP_NO_DEPENDENCIES="True"\n-export PIP_IGNORE_INSTALLED="True"\n-export PIP_CACHE_DIR="/opt/conda/conda-bld/jbrowse2_1726856947541/pip_cache"\n-export PIP_NO_INDEX="True"\n-eval "$(\'/opt/conda/bin/python\' -m conda shell.bash hook)"\n-conda activate "/home/ross/miniconda3/envs/mulled-v1-ead19212d339c2197ed3232dcd8366627d23ccb1cf4fb8ae3186545effdca881"\n-conda activate --stack "/opt/conda/conda-bld/jbrowse2_1726856947541/_build_env"\n'

diff -r cec274db51c0 -r ed3a21033188 x/conda_build.sh
--- a/x/conda_build.sh Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,20 +0,0 @@
-if [ -z ${CONDA_BUILD+x} ]; then
- source /opt/conda/conda-bld/jbrowse2_1726856947541/work/build_env_setup.sh
-fi
-#!/bin/bash
-
-# Place the jbrowse2 www content in the conda package
-mkdir -p $PREFIX/opt/jbrowse2/
-cp -r * $PREFIX/opt/jbrowse2/
-
-# Set an env var for people willing to find the jbrowse2 www content
-mkdir -p $PREFIX/etc/conda/activate.d/
-echo "export JBROWSE2_SOURCE_DIR=$PREFIX/opt/jbrowse2" > $PREFIX/etc/conda/activate.d/jbrowse2-sourcedir.sh
-chmod a+x $PREFIX/etc/conda/activate.d/jbrowse2-sourcedir.sh
-
-mkdir -p $PREFIX/etc/conda/deactivate.d/
-echo "unset JBROWSE2_SOURCE_DIR" > $PREFIX/etc/conda/deactivate.d/jbrowse2-sourcedir.sh
-chmod a+x $PREFIX/etc/conda/deactivate.d/jbrowse2-sourcedir.sh
-
-# Install the CLI
-npm install --prefix=${PREFIX} -g @jbrowse/cli@${PKG_VERSION}

diff -r cec274db51c0 -r ed3a21033188 x/config.json
--- a/x/config.json Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,1007 +0,0 @@\n-{\n- "plugins": [\n- {\n- "name": "BedScorePlugin",\n- "umdLoc": {\n- "uri": "bedscoreplugin.js"\n- }\n- },\n- {\n- "name": "MafViewer",\n- "url": "https://unpkg.com/jbrowse-plugin-mafviewer/dist/jbrowse-plugin-mafviewer.umd.production.min.js"\n- }\n- ],\n- "configuration": {\n- "disableAnalytics": false,\n- "theme": {\n- "palette": {\n- "primary": {\n- "main": "#0d233f"\n- },\n- "secondary": {\n- "main": "#721e63"\n- },\n- "tertiary": {\n- "main": "#135560"\n- },\n- "quaternary": {\n- "main": "#ffb11d"\n- }\n- },\n- "typography": {\n- "fontSize": 10\n- }\n- }\n- },\n- "defaultSession": {\n- "name": "New test session",\n- "views": [\n- {\n- "type": "LinearGenomeView",\n- "offsetPx": 0,\n- "bpPerPx": 50,\n- "minimized": false,\n- "tracks": [\n- {\n- "type": "FeatureTrack",\n- "configuration": "merlin.gff3_0",\n- "displays": [\n- {\n- "type": "LinearBasicDisplay",\n- "displayId": "merlin.gff3_0-LinearBasicDisplay",\n- "trackShowLabels": false,\n- "trackShowDescriptions": false,\n- "configuration": "merlin.gff3_0-LinearBasicDisplay"\n- }\n- ]\n- },\n- {\n- "type": "QuantitativeTrack",\n- "configuration": "merlin.bw_1",\n- "displays": [\n- {\n- "type": "LinearWiggleDisplay",\n- "displayId": "merlin.bw_1-LinearWiggleDisplay",\n- "color": "#135560",\n- "autoscale": "globalsd",\n- "resolution": 1,\n- "summaryScoreMode": "whiskers",\n- "filled": false,\n- "scaleType": "linear",\n- "displayCrossHatches": false,\n- "configuration": "merlin.bw_1-LinearWiggleDisplay"\n- }\n- ]\n- },\n- {\n- "type": "FeatureTrack",\n- "configuration": "test-6.bed_2",\n- "displays": [\n- {\n- "type": "LinearBasicDisplay",\n- "displayId": "test-6.bed_2-LinearBasicDisplay",\n- "trackShowLabels": false,\n- "trackShowDescriptions": false,\n- "configuration": "test-6.bed_2-LinearBasicDisplay"\n- }\n- ]\n- },\n- {\n- "type": "VariantTrack",\n- "configuration": "merlin.vcf_3",\n- "displays": [\n- {\n- "type": "LinearVariantDisplay",\n- "displayId": "merlin.vcf_3-LinearVariantDisplay",\n- "trackShowLabels": false,\n- "trackShowDescriptions": false,\n- "configuration": "merlin.vcf_3-LinearVariantDisplay"\n- }\n- ]\n- },\n- {\n- "type": "AlignmentsTrack",\n- "configuration": "merlin.cram_4",\n- "displays": [\n- {\n- "type": "LinearAlignmentsDisplay",\n- "displayId": "merlin.cram_4-LinearAlignmentsDisplay",\n- "configuration": "merlin.cram_4-LinearAlignmentsDisplay"\n- }\n- ]\n- },\n- {\n- "type": "AlignmentsTrack",\n- "configuration": "merlin-sample.bam_5",\n- "displays": [\n- {\n- "type": "LinearAlignmentsDisplay",\n- "displayId": "merlin-sample.bam_5-LinearAlignmentsDisplay",\n- "configuration": "merlin-sample.bam_5-LinearAlignmentsDisplay"\n- }\n- ]\n- },\n- {\n- "type": "MafTrack",\n- "configuration": "merlinlastz.maf_6",\n- "displays": [\n- {\n- "type": "LinearBasicDisplay",\n- "displayId": "'..b' "displays": [\n- {\n- "type": "LinearReferenceSequenceDisplay",\n- "displayId": "Ppersica1.fa-LinearReferenceSequenceDisplay"\n- },\n- {\n- "type": "LinearGCContentDisplay",\n- "displayId": "Ppersica1.fa-LinearGCContentDisplay"\n- }\n- ]\n- },\n- {\n- "name": "Vvinifera1.fa",\n- "sequence": {\n- "type": "ReferenceSequenceTrack",\n- "trackId": "Vvinifera1.fa",\n- "adapter": {\n- "type": "BgzipFastaAdapter",\n- "fastaLocation": {\n- "uri": "Vvinifera1.fa.fa.gz"\n- },\n- "faiLocation": {\n- "uri": "Vvinifera1.fa.fa.gz.fai"\n- },\n- "gziLocation": {\n- "uri": "Vvinifera1.fa.fa.gz.gzi"\n- }\n- }\n- },\n- "displays": [\n- {\n- "type": "LinearReferenceSequenceDisplay",\n- "displayId": "Vvinifera1.fa-LinearReferenceSequenceDisplay"\n- },\n- {\n- "type": "LinearGCContentDisplay",\n- "displayId": "Vvinifera1.fa-LinearGCContentDisplay"\n- }\n- ]\n- },\n- {\n- "name": "arabidopsis.URI",\n- "sequence": {\n- "type": "ReferenceSequenceTrack",\n- "trackId": "arabidopsis.URI",\n- "adapter": {\n- "type": "BgzipFastaAdapter",\n- "fastaLocation": {\n- "uri": "https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabidopsis.fa.gz"\n- },\n- "faiLocation": {\n- "uri": "https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabidopsis.fa.gz.fai"\n- },\n- "gziLocation": {\n- "uri": "https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabidopsis.fa.gz.gzi"\n- }\n- }\n- },\n- "displays": [\n- {\n- "type": "LinearReferenceSequenceDisplay",\n- "displayId": "arabidopsis.URI-LinearReferenceSequenceDisplay"\n- },\n- {\n- "type": "LinearGCContentDisplay",\n- "displayId": "arabidopsis.URI-LinearGCContentDisplay"\n- }\n- ]\n- },\n- {\n- "name": "Vvinifera1.URI",\n- "sequence": {\n- "type": "ReferenceSequenceTrack",\n- "trackId": "Vvinifera1.URI",\n- "adapter": {\n- "type": "BgzipFastaAdapter",\n- "fastaLocation": {\n- "uri": "https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Vvinifera1.fa.gz"\n- },\n- "faiLocation": {\n- "uri": "https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Vvinifera1.fa.gz.fai"\n- },\n- "gziLocation": {\n- "uri": "https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Vvinifera1.fa.gz.gzi"\n- }\n- }\n- },\n- "displays": [\n- {\n- "type": "LinearReferenceSequenceDisplay",\n- "displayId": "Vvinifera1.URI-LinearReferenceSequenceDisplay"\n- },\n- {\n- "type": "LinearGCContentDisplay",\n- "displayId": "Vvinifera1.URI-LinearGCContentDisplay"\n- }\n- ]\n- },\n- {\n- "name": "hg38",\n- "sequence": {\n- "type": "ReferenceSequenceTrack",\n- "trackId": "hg38",\n- "adapter": {\n- "type": "BgzipFastaAdapter",\n- "fastaLocation": {\n- "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz"\n- },\n- "faiLocation": {\n- "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz.fai"\n- },\n- "gziLocation": {\n- "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz.gzi"\n- }\n- }\n- },\n- "displays": [\n- {\n- "type": "LinearReferenceSequenceDisplay",\n- "displayId": "hg38-LinearReferenceSequenceDisplay"\n- },\n- {\n- "type": "LinearGCContentDisplay",\n- "displayId": "hg38-LinearGCContentDisplay"\n- }\n- ]\n- }\n- ]\n-}\n\\ No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/dm3.fa.fa.gz

Binary file x/dm3.fa.fa.gz has changed

diff -r cec274db51c0 -r ed3a21033188 x/dm3.fa.fa.gz.fai
--- a/x/dm3.fa.fa.gz.fai Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-NT_037436.4 28110227 51 70 71

diff -r cec274db51c0 -r ed3a21033188 x/dm3.fa.fa.gz.gzi

Binary file x/dm3.fa.fa.gz.gzi has changed

diff -r cec274db51c0 -r ed3a21033188 x/dm3test.cool_9.hic

Binary file x/dm3test.cool_9.hic has changed

diff -r cec274db51c0 -r ed3a21033188 x/galaxy.xml
--- a/x/galaxy.xml Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,628 +0,0 @@\n-<?xml version="1.0"?>\n-<root>\n- <metadata>\n- <general>\n- <defaultLocation></defaultLocation>\n- <zipOut>true</zipOut>\n- <bpPerPx>50</bpPerPx>\n- <analytics>false</analytics>\n- <primary_color>#0d233f</primary_color>\n- <secondary_color>#721e63</secondary_color>\n- <tertiary_color>#135560</tertiary_color>\n- <quaternary_color>#ffb11d</quaternary_color>\n- <font_size>10</font_size>\n- <session_name>New test session</session_name>\n- </general>\n- <galaxyUrl>http://localhost:8080</galaxyUrl>\n- </metadata>\n- <assembly>\n- <metadata>\n- <genomes>\n- <genome path="/tmp/tmpus622kw5/files/7/4/8/dataset_748d2461-ea0f-4e92-b129-e680b76d4c81.dat" label="Merlin" useuri="no">\n- <metadata>\n-\n- <dataset id="801225f8dc4ca2f7"\n- hid="1"\n- size="171.6 KB"\n- edam_format="format_1929"\n- file_ext="fasta"\n- dname = "Merlin"\n- />\n- <history\n- user_email="planemo@galaxyproject.org"\n- user_id="1"\n- display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>\n- id="801225f8dc4ca2f7"\n- />\n- <metadata\n- dbkey="?"\n- data_lines="2881"\n- sequences="1"\n- />\n- <tool\n- tool_id="upload1"\n- tool_version="1.1.7"\n- />\n- </metadata>\n- </genome>\n- </genomes>\n- </metadata>\n- <tracks>\n- <track cat="Assembly properties" format="gff" visibility="default_on">\n- <files>\n- <trackFile path="/tmp/tmpus622kw5/files/b/7/d/dataset_b7de2a4d-8123-493d-99ad-6f251912ae1c.dat" ext="gff3" label="merlin.gff3" useuri="no">\n- <metadata>\n- <dataset id="f899122287bdd0b2" hid="2"\n- size="5.0 KB"\n- edam_format="format_1975"\n- file_ext="gff3" />\n- <history id="801225f8dc4ca2f7"\n- user_email="planemo@galaxyproject.org"\n- user_id="1"\n- display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>\n- <metadata\n- dbkey="?"\n- data_lines="9"\n- comment_lines="10"\n- columns="9"\n- column_names="[]"\n- delimiter="__tc__"\n- attributes="23"\n- />\n- <tool\n- tool_id="upload1"\n- tool_version="1.1.7"\n- />\n- </metadata>\n- </trackFile>\n- </files>\n- <options>\n- <style>\n- <type>LinearBasicDisplay</type>\n- <trackShowLabels>false</trackShowLabels>\n- <trackShowDescriptions>false</trackShowDescriptions>\n- </style>\n- '..b' <genome>\n- https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabidopsis.fa.gz ~ arabidopsis.URI,\n- https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Vvinifera1.fa.gz ~ Vvinifera1.URI,\n- </genome>\n- <useuri>\n- true\n- </useuri>\n- </paf>\n- </options>\n- </track>\n- <track cat="Assembly properties" format="paf" visibility="default_on">\n- <files>\n- <trackFile path="/tmp/tmpus622kw5/files/2/7/2/dataset_272188a9-0367-4677-9b28-ad5e84aceb99.dat" ext="paf" label="arabgrapepeach.paf" useuri="no">\n- <metadata>\n- <dataset id="edaefaa2c8238b09" hid="16"\n- size="12.8 MB"\n- edam_format="format_2330"\n- file_ext="paf" />\n- <history id="801225f8dc4ca2f7"\n- user_email="planemo@galaxyproject.org"\n- user_id="1"\n- display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>\n- <metadata\n- dbkey="?"\n- data_lines="129777"\n- />\n- <tool\n- tool_id="upload1"\n- tool_version="1.1.7"\n- />\n- </metadata>\n- </trackFile>\n- </files>\n- <options>\n- <style>\n- </style>\n- <paf>\n- <genome>\n- /tmp/tmpus622kw5/files/e/4/4/dataset_e44ca09b-d9ff-4a99-a4cb-e50f24a66ff9.dat ~ Vvinifera1.fa,\n- </genome>\n- <useuri>\n- false\n- </useuri>\n- </paf>\n- </options>\n- </track>\n- </tracks>\n- </assembly>\n- <assembly>\n- <metadata>\n- <genomes>\n- <genome path="https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz" label="hg38" useuri="yes">\n- <metadata>\n- <dataset\n- dname = "hg38" />\n- </metadata>\n- </genome>\n- </genomes>\n- </metadata>\n- <tracks>\n- <track cat="Assembly properties" format="hic" visibility="default_on">\n- <files>\n- <trackFile path="https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic" ext="hic"\n- label="humanhic" useuri="yes">\n- <metadata>\n- <dataset id = "https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic" />\n- </metadata>\n- </trackFile>\n- </files>\n- <options>\n- <style>\n- <type>LinearHicDisplay</type>\n- </style>\n- <hic>\n- </hic>\n- </options>\n- </track>\n- </tracks>\n- </assembly>\n-</root>\n'

diff -r cec274db51c0 -r ed3a21033188 x/index.html
--- a/x/index.html Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-<!doctype html><html lang="en"><head><meta charset="utf-8"/><link rel="shortcut icon" href="./favicon.ico"/><meta name="viewport" content="width=device-width,initial-scale=1"/><meta name="theme-color" content="#000000"/><meta name="description" content="A fast and flexible genome browser"/><link rel="manifest" href="./manifest.json"/><title>JBrowse</title><script defer="defer" src="static/js/main.1532dd54.js"></script></head><body style="overscroll-behavior:none"><noscript>You need to enable JavaScript to run this app.</noscript><div id="root"></div></body></html>
\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/jb2_webserver.py
--- a/x/jb2_webserver.py Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,187 +0,0 @@
-#!/usr/bin/env python3
-# spec: simplest python web server with range support and multithreading that takes root path,
-# port and bind address as command line arguments; by default uses the current dir as webroot,
-# port 8000 and bind address of 0.0.0.0
-# borrowed from https://github.com/danvk/RangeHTTPServer
-# and reborrowed from https://gist.github.com/glowinthedark/b99900abe935e4ab4857314d647a9068
-#
-# The Apache 2.0 license copy in this repository is distributed with this code in accordance with that licence.
-# https://www.apache.org/licenses/LICENSE-2.0.txt
-# This part is not MIT licenced like the other components.
-
-# APPENDIX: How to apply the Apache License to your work.
-
-# To apply the Apache License to your work, attach the following
-# boilerplate notice, with the fields enclosed by brackets "[]"
-# replaced with your own identifying information. (Don't include
-# the brackets!)  The text should be enclosed in the appropriate
-# comment syntax for the file format. We also recommend that a
-# file or class name and description of purpose be included on the
-# same "printed page" as the copyright notice for easier
-# identification within third-party archives.
-
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-
-# http://www.apache.org/licenses/LICENSE-2.0
-
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-
-import argparse
-import functools
-import os
-import re
-import socketserver
-import webbrowser
-from http.server import SimpleHTTPRequestHandler
-
-
-DEFAULT_PORT = 8081
-
-
-def copy_byte_range(infile, outfile, start=None, stop=None, bufsize=16 * 1024):
-    """Like shutil.copyfileobj, but only copy a range of the streams.
-
-    Both start and stop are inclusive.
-    """
-    if start is not None:
-        infile.seek(start)
-    while 1:
-        to_read = min(bufsize, stop + 1 - infile.tell() if stop else bufsize)
-        buf = infile.read(to_read)
-        if not buf:
-            break
-        outfile.write(buf)
-
-
-BYTE_RANGE_RE = re.compile(r"bytes=(\d+)-(\d+)?$")
-
-
-def parse_byte_range(byte_range):
-    """Returns the two numbers in 'bytes=123-456' or throws ValueError.
-
-    The last number or both numbers may be None.
-    """
-    if byte_range.strip() == "":
-        return None, None
-
-    m = BYTE_RANGE_RE.match(byte_range)
-    if not m:
-        raise ValueError("Invalid byte range %s" % byte_range)
-
-    first, last = [x and int(x) for x in m.groups()]
-    if last and last < first:
-        raise ValueError("Invalid byte range %s" % byte_range)
-    return first, last
-
-
-class RangeRequestHandler(SimpleHTTPRequestHandler):
-    """Adds support for HTTP 'Range' requests to SimpleHTTPRequestHandler
-
-    The approach is to:
-    - Override send_head to look for 'Range' and respond appropriately.
-    - Override copyfile to only transmit a range when requested.
-    """
-
-    def handle(self):
-        try:
-            SimpleHTTPRequestHandler.handle(self)
-        except Exception:
-            # ignored, thrown whenever the client aborts streaming (broken pipe)
-            pass
-
-    def send_head(self):
-        if "Range" not in self.headers:
-            self.range = None
-            return SimpleHTTPRequestHandler.send_head(self)
-        try:
-            self.range = parse_byte_range(self.headers["Range"])
-        except ValueError:
-            self.send_error(400, "Invalid byte range")
-            return None
-        first, last = self.range
-
-        # Mirroring SimpleHTTPServer.py here
-        path = self.translate_path(self.path)
-        f = None
-        ctype = self.guess_type(path)
-        try:
-            f = open(path, "rb")
-        except IOError:
-            self.send_error(404, "File not found")
-            return None
-
-        fs = os.fstat(f.fileno())
-        file_len = fs[6]
-        if first >= file_len:
-            self.send_error(416, "Requested Range Not Satisfiable")
-            return None
-
-        self.send_response(206)
-        self.send_header("Content-type", ctype)
-
-        if last is None or last >= file_len:
-            last = file_len - 1
-        response_length = last - first + 1
-
-        self.send_header("Content-Range", "bytes %s-%s/%s" % (first, last, file_len))
-        self.send_header("Content-Length", str(response_length))
-        self.send_header("Last-Modified", self.date_time_string(fs.st_mtime))
-        self.end_headers()
-        return f
-
-    def end_headers(self):
-        self.send_header("Accept-Ranges", "bytes")
-        return SimpleHTTPRequestHandler.end_headers(self)
-
-    def copyfile(self, source, outputfile):
-        if not self.range:
-            return SimpleHTTPRequestHandler.copyfile(self, source, outputfile)
-
-        # SimpleHTTPRequestHandler uses shutil.copyfileobj, which doesn't let
-        # you stop the copying before the end of the file.
-        start, stop = self.range  # set in send_head()
-        copy_byte_range(source, outputfile, start, stop)
-
-
-class ThreadedTCPServer(socketserver.ThreadingMixIn, socketserver.TCPServer):
-    allow_reuse_address = True
-
-
-if __name__ == "__main__":
-    parser = argparse.ArgumentParser(
-        description="Tiny Python Web Server supporting range requests, for local viewing of unzipped Galaxy JBrowse2 configurations"
-    )
-    parser.add_argument(
-        "--root",
-        default=os.getcwd(),
-        help="Root path to serve files from (default: current working directory)",
-    )
-    parser.add_argument(
-        "--port",
-        type=int,
-        default=DEFAULT_PORT,
-        help=f"Port to listen on (default: {DEFAULT_PORT})",
-    )
-    parser.add_argument(
-        "--bind",
-        default="127.0.0.1",
-        help="IP address to bind to (default: 127.0.0.1 - use 0.0.0.0 to allow access on your network)",
-    )
-    args = parser.parse_args()
-
-    handler = functools.partial(RangeRequestHandler, directory=args.root)
-
-    webbrowser.open(f"http://{args.bind}:{args.port}")
-
-    with ThreadedTCPServer((args.bind, args.port), handler) as httpd:
-        print(
-            f"Serving HTTP on {args.bind} port {args.port} (http://{args.bind}:{args.port}/)"
-        )
-        httpd.serve_forever()

diff -r cec274db51c0 -r ed3a21033188 x/manifest.json
--- a/x/manifest.json Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,15 +0,0 @@
-{
-  "short_name": "JBrowse",
-  "name": "JBrowse",
-  "icons": [
-    {
-      "src": "favicon.ico",
-      "sizes": "64x64 48x48 32x32 24x24 16x16",
-      "type": "image/x-icon"
-    }
-  ],
-  "start_url": ".",
-  "display": "standalone",
-  "theme_color": "#396494",
-  "background_color": "#fafafa"
-}

diff -r cec274db51c0 -r ed3a21033188 x/merlin-sample.bam_5

Binary file x/merlin-sample.bam_5 has changed

diff -r cec274db51c0 -r ed3a21033188 x/merlin-sample.bam_5.bai

Binary file x/merlin-sample.bam_5.bai has changed

diff -r cec274db51c0 -r ed3a21033188 x/merlin.blastxml_7.gz

Binary file x/merlin.blastxml_7.gz has changed

diff -r cec274db51c0 -r ed3a21033188 x/merlin.blastxml_7.gz.tbi

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diff -r cec274db51c0 -r ed3a21033188 x/merlin.bw_1

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diff -r cec274db51c0 -r ed3a21033188 x/merlin.cram_4

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diff -r cec274db51c0 -r ed3a21033188 x/merlin.cram_4.crai

Binary file x/merlin.cram_4.crai has changed

diff -r cec274db51c0 -r ed3a21033188 x/merlin.gff3_0.gz

Binary file x/merlin.gff3_0.gz has changed

diff -r cec274db51c0 -r ed3a21033188 x/merlin.gff3_0.gz.tbi

Binary file x/merlin.gff3_0.gz.tbi has changed

diff -r cec274db51c0 -r ed3a21033188 x/merlin.vcf_3

Binary file x/merlin.vcf_3 has changed

diff -r cec274db51c0 -r ed3a21033188 x/merlin.vcf_3.tbi

Binary file x/merlin.vcf_3.tbi has changed

diff -r cec274db51c0 -r ed3a21033188 x/merlinlastz.maf_6.sorted.bed
--- a/x/merlinlastz.maf_6.sorted.bed Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,6 +0,0 @@
-Merlin 1320 1380 Merlin_1 5595 Merlin.Merlin:1320:60:+:172788:ATGTAAGCTCAGGAGCTCCACACGCAACAGGAACACAACCTGTGAACATTATCACAGTAT,Merlin1.Merlin:0:60:+:60:ATGTAAGCTCAGGAGCTCCACACGCAACAGGAACACAACCTGTGAACATTATCACAGTAT
-Merlin 4020 4080 Merlin_2 5667 Merlin.Merlin:4020:60:+:172788:ATGAATTTATCAGTCCAATACTTAAAATGAATACGAAGTAAATCTATGCCTAATACTAAT,Merlin2.Merlin:0:60:+:60:ATGAATTTATCAGTCCAATACTTAAAATGAATACGAAGTAAATCTATGCCTAATACTAAT
-Merlin 5220 5280 Merlin_3 5640 Merlin.Merlin:5220:60:+:172788:TAATCAACGTGTGATGCTTCAAGCCAAGCTTAGGAATAGAAATGGTTTTGCCATTGACTT,Merlin3.Merlin:0:60:+:60:TAATCAACGTGTGATGCTTCAAGCCAAGCTTAGGAATAGAAATGGTTTTGCCATTGACTT
-Merlin 7740 7800 Merlin_4 5649 Merlin.Merlin:7740:60:+:172788:AAAAGCTTATTGCTTAAGCCTACAGTTAAACTCGCTATTCCAGTTAAATGCGATAAATGT,Merlin4.Merlin:0:60:+:60:AAAAGCTTATTGCTTAAGCCTACAGTTAAACTCGCTATTCCAGTTAAATGCGATAAATGT
-Merlin 9720 9780 Merlin_5 5658 Merlin.Merlin:9720:60:+:172788:TTTTCTTTGCTAATTTAACACCAAGAGCTGCAATCCATTGGTTTCTTCGTTTATATCCTG,Merlin5.Merlin:0:60:+:60:TTTTCTTTGCTAATTTAACACCAAGAGCTGCAATCCATTGGTTTCTTCGTTTATATCCTG
-Merlin 10380 10440 Merlin_6 5658 Merlin.Merlin:10380:60:+:172788:ATACTGCATCCTTTTGATACCAATGCGGTTCAATTTGAGTGTTACCAGAGTATATCTTGA,Merlin6.Merlin:0:60:+:60:ATACTGCATCCTTTTGATACCAATGCGGTTCAATTTGAGTGTTACCAGAGTATATCTTGA

diff -r cec274db51c0 -r ed3a21033188 x/merlinlastz.maf_6.sorted.bed.gz

Binary file x/merlinlastz.maf_6.sorted.bed.gz has changed

diff -r cec274db51c0 -r ed3a21033188 x/merlinlastz.maf_6.sorted.bed.gz.tbi

Binary file x/merlinlastz.maf_6.sorted.bed.gz.tbi has changed

diff -r cec274db51c0 -r ed3a21033188 x/metadata_conda_debug.yaml
--- a/x/metadata_conda_debug.yaml Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,33 +0,0 @@
-package:
-  name: jbrowse2
-  version: 2.15.4
-source:
-  sha256: fa0a6163dab65d1705c1968cc41adc0f6b035a8fbc572b7ddff12721b5b58642
-  url: https://github.com/GMOD/jbrowse-components/releases/download/v2.15.4/jbrowse-web-v2.15.4.zip
-build:
-  noarch: generic
-  number: '0'
-  run_exports:
-    - jbrowse2
-requirements:
-  host:
-    - nodejs
-  run:
-    - nodejs
-    - bcftools
-    - gff3sort
-    - htslib
-    - samtools
-test:
-  commands:
-    - jbrowse help | grep "command line tool for working with JBrowse"
-about:
-  home: https://jbrowse.org/
-  license: Apache-2.0
-  license_family: Apache
-  summary: The JBrowse 2 Genome Browser
-extra:
-  final: false
-  identifiers:
-    - biotools:jbrowse
-    - doi:10.1101/gr.094607.109

diff -r cec274db51c0 -r ed3a21033188 x/peach-grape-map.paf_10
--- a/x/peach-grape-map.paf_10 Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,9291 +0,0 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Binary file x/peach-grape-map.paf_10.pif.gz.tbi has changed

diff -r cec274db51c0 -r ed3a21033188 x/static/css/3120.6d3f3959.chunk.css
--- a/x/static/css/3120.6d3f3959.chunk.css Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/css/3120.6d3f3959.chunk.css.map
--- a/x/static/css/3120.6d3f3959.chunk.css.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/1157.c0d4652e.chunk.js
--- a/x/static/js/1157.c0d4652e.chunk.js Fri Oct 18 11:57:55 2024 +0000
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--- a/x/static/js/1157.c0d4652e.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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Container.propTypes /* remove-proptypes */ = {\\n // \xe2\x94\x8c\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80 Warning \xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x90\\n // \xe2\x94\x82 These PropTypes are generated from the TypeScript type definitions. \xe2\x94\x82\\n // \xe2\x94\x82 To update them, edit the d.ts file and run `pnpm proptypes`. \xe2\x94\x82\\n // \xe2\x94\x94\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x98\\n /**\\n * @ignore\\n */\\n children: PropTypes.node,\\n /**\\n * Override or extend the styles applied to the component.\\n */\\n classes: PropTypes.object,\\n /**\\n * The component used for the root node.\\n * Either a string to use a HTML element or a component.\\n */\\n component: PropTypes.elementType,\\n /**\\n * If `true`, the left and right padding is removed.\\n * @default false\\n */\\n disableGutters: PropTypes.bool,\\n /**\\n * Set the max-width to match the min-width of the current breakpoint.\\n * This is useful if you\'d prefer to design for a fixed set of sizes\\n * instead of trying to accommodate a fully fluid viewport.\\n * It\'s fluid by default.\\n * @default false\\n */\\n fixed: PropTypes.bool,\\n /**\\n * Determine the max-width of the container.\\n * The container width grows with the size of the screen.\\n * Set to `false` to disable `maxWidth`.\\n * @default \'lg\'\\n */\\n maxWidth: PropTypes /* @typescript-to-proptypes-ignore */.oneOfType([PropTypes.oneOf([\'xs\', \'sm\', \'md\', \'lg\', \'xl\', false]), PropTypes.string]),\\n /**\\n * The system prop that allows defining system overrides as well as additional CSS styles.\\n */\\n sx: PropTypes.oneOfType([PropTypes.arrayOf(PropTypes.oneOfType([PropTypes.func, PropTypes.object, PropTypes.bool])), PropTypes.func, PropTypes.object])\\n} : void 0;\\nexport default Container;","import generateUtilityClasses from \'@mui/utils/generateUtilityClasses\';\\nimport generateUtilityClass from \'@mui/utils/generateUtilityClass\';\\nexport function getContainerUtilityClass(slot) {\\n return generateUtilityClass(\'MuiContainer\', slot);\\n}\\nconst containerClasses = generateUtilityClasses(\'MuiContainer\', [\'root\', \'disableGutters\', \'fixed\', \'maxWidthXs\', \'maxWidthSm\', \'maxWidthMd\', \'maxWidthLg\', \'maxWidthXl\']);\\nexport default containerClasses;","import createStyled from \\"../createStyled/index.js\\";\\nconst styled = createStyled();\\nexport default styled;"],"names":["defaultTheme","createTheme","defaultCreateStyledComponent","name","slot","overridesResolver","props","styles","ownerState","root","capitalize","String","maxWidth","fixed","disableGutters","useThemePropsDefault","inProps","useThemeProps","Container","options","createStyledComponent","componentName","ContainerRoot","theme","width","marginLeft","boxSizing","marginRight","paddingLeft","spacing","paddingRight","breakpoints","up","Object","keys","values","reduce","acc","breakpointValueKey","breakpoint","value","unit","Math","max","xs","ref","className","component","classes","classesProp","other","slots","composeClasses","generateUtilityClass","useUtilityClasses","as","clsx","createContainer","getContainerUtilityClass","generateUtilityClasses"],"sourceRoot":""}\n\\ No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/1189.f18c6e1f.chunk.js
--- a/x/static/js/1189.f18c6e1f.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/1189.f18c6e1f.chunk.js.map
--- a/x/static/js/1189.f18c6e1f.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/12.c0c7bdf9.chunk.js
--- a/x/static/js/12.c0c7bdf9.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/12.c0c7bdf9.chunk.js.map
--- a/x/static/js/12.c0c7bdf9.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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Defaults to \'material-icons\', but can be changed to any\\n * other base class that suits the icon font you\'re using (for example material-icons-rounded, fas, etc).\\n * @default \'material-icons\'\\n */\\n baseClassName: PropTypes.string,\\n /**\\n * The name of the icon font ligature.\\n */\\n children: PropTypes.node,\\n /**\\n * Override or extend the styles applied to the component.\\n */\\n classes: PropTypes.object,\\n /**\\n * @ignore\\n */\\n className: PropTypes.string,\\n /**\\n * The color of the component.\\n * It supports both default and custom theme colors, which can be added as shown in the\\n * [palette customization guide](https://mui.com/material-ui/customization/palette/#custom-colors).\\n * @default \'inherit\'\\n */\\n color: PropTypes /* @typescript-to-proptypes-ignore */.oneOfType([PropTypes.oneOf([\'inherit\', \'action\', \'disabled\', \'primary\', \'secondary\', \'error\', \'info\', \'success\', \'warning\']), PropTypes.string]),\\n /**\\n * The component used for the root node.\\n * Either a string to use a HTML element or a component.\\n */\\n component: PropTypes.elementType,\\n /**\\n * The fontSize applied to the icon. Defaults to 24px, but can be configure to inherit font size.\\n * @default \'medium\'\\n */\\n fontSize: PropTypes /* @typescript-to-proptypes-ignore */.oneOfType([PropTypes.oneOf([\'inherit\', \'large\', \'medium\', \'small\']), PropTypes.string]),\\n /**\\n * The system prop that allows defining system overrides as well as additional CSS styles.\\n */\\n sx: PropTypes.oneOfType([PropTypes.arrayOf(PropTypes.oneOfType([PropTypes.func, PropTypes.object, PropTypes.bool])), PropTypes.func, PropTypes.object])\\n} : void 0;\\nif (Icon) {\\n Icon.muiName = \'Icon\';\\n}\\nexport default Icon;"],"names":["getIconUtilityClass","slot","generateUtilityClass","generateUtilityClasses","IconRoot","styled","name","overridesResolver","props","styles","ownerState","root","color","capitalize","fontSize","memoTheme","theme","userSelect","width","height","overflow","display","textAlign","flexShrink","variants","style","typography","pxToRem","vars","palette","action","active","disabled","undefined","Object","entries","filter","createSimplePaletteValueFilter","map","main","Icon","inProps","ref","baseClassName","className","component","Component","other","classes","slots","composeClasses","useUtilityClasses","as","clsx","muiName"],"sourceRoot":""}\n\\ No newline at end of file\n'

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--- a/x/static/js/120.a447052d.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/1260.ee4ecbf4.chunk.js
--- a/x/static/js/1260.ee4ecbf4.chunk.js Fri Oct 18 11:57:55 2024 +0000
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We recommend checking https://caniuse.com/?search=flex%20gap before using this flag.\\n *\\n * To enable this flag globally, follow the [theme\'s default props](https://mui.com/material-ui/customization/theme-components/#default-props) configuration.\\n * @default false\\n */\\n useFlexGap: PropTypes.bool\\n} : void 0;\\nexport default Stack;","import generateUtilityClasses from \'@mui/utils/generateUtilityClasses\';\\nimport generateUtilityClass from \'@mui/utils/generateUtilityClass\';\\nexport function getStackUtilityClass(slot) {\\n return generateUtilityClass(\'MuiStack\', slot);\\n}\\nconst stackClasses = generateUtilityClasses(\'MuiStack\', [\'root\']);\\nexport default stackClasses;","import createStyled from \\"../createStyled/index.js\\";\\nconst styled = createStyled();\\nexport default styled;"],"names":["defaultTheme","createTheme","defaultCreateStyledComponent","name","slot","overridesResolver","props","styles","root","useThemePropsDefault","useThemeProps","joinChildren","children","separator","childrenArray","toArray","filter","Boolean","reduce","output","child","index","push","length","key","style","ownerState","theme","display","flexDirection","values","direction","breakpoints","propValue","spacing","transformer","base","Object","keys","acc","breakpoint","directionValues","spacingValues","forEach","previousDirectionValue","styleFromPropValue","useFlexGap","gap","margin","row","column","deepmerge","Stack","options","createStyledComponent","componentName","StackRoot","inProps","ref","themeProps","extendSxProp","component","divider","className","other","classes","composeClasses","generateUtilityClass","as","clsx","createStack"],"sourceRoot":""}\n\\ No newline at end of file\n'

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--- a/x/static/js/1266.cd6d9354.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/1266.cd6d9354.chunk.js.map
--- a/x/static/js/1266.cd6d9354.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/1281.1d836fc4.chunk.js
--- a/x/static/js/1281.1d836fc4.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/1281.1d836fc4.chunk.js.map
--- a/x/static/js/1281.1d836fc4.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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A track will be created with the\n resulting matches once submitted. You can also supply regex style\n expressions e.g. AACT(C|T).\n </Typography>\n <TextField\n value={value}\n onChange={e => {\n setValue(e.target.value)\n }}\n helperText=\"Sequence search pattern\"\n />\n <FormGroup>\n <FormControlLabel\n control={\n <Checkbox\n checked={searchForward}\n onChange={event => {\n setSearchForward(event.target.checked)\n }}\n />\n }\n label=\"Search forward strand\"\n />\n <FormControlLabel\n control={\n <Checkbox\n checked={searchReverse}\n onChange={event => {\n setSearchReverse(event.target.checked)\n }}\n />\n }\n label=\"Search reverse strand\"\n />\n <FormControlLabel\n control={\n <Checkbox\n checked={caseInsensitive}\n onChange={event => {\n setCaseInsensitive(event.target.checked)\n }}\n />\n }\n label=\"Case insensitive\"\n />\n </FormGroup>\n {error ? <Typography color=\"error\">{`${error}`}</Typography> : null}\n </DialogContent>\n <DialogActions>\n <Button\n onClick={() => {\n if (value) {\n const trackId = `sequence_search_${+Date.now()}`\n const session = getSession(model)\n const { assemblyManager } = session\n const assemblyName = model.assemblyNames[0]!\n if (isSessionWithAddTracks(session)) {\n session.addTrackConf({\n trackId,\n name: `Sequence search ${value}`,\n assemblyNames: [assemblyName],\n type: 'FeatureTrack',\n adapter: {\n type: 'SequenceSearchAdapter',\n search: value,\n searchForward,\n searchReverse,\n caseInsensitive,\n sequenceAdapter: getSnapshot(\n assemblyManager.get(assemblyName)?.configuration.sequence\n .adapter,\n ),\n },\n })\n model.showTrack(trackId)\n }\n }\n handleClose()\n }}\n variant=\"contained\"\n color=\"primary\"\n >\n Submit\n </Button>\n\n <Button\n onClick={() => {\n handleClose()\n }}\n variant=\"contained\"\n color=\"secondary\"\n >\n Close\n </Button>\n </DialogActions>\n </Dialog>\n )\n})\n\nexport default SequenceSearchDialog\n"],"names":["useStyles","makeStyles","dialogContent","width","observer","model","handleClose","classes","value","setValue","useState","searchForward","setSearchForward","searchReverse","setSearchReverse","caseInsensitive","setCaseInsensitive","error","RegExp","e","React","Dialog","maxWidth","open","onClose","title","DialogContent","className","Typography","TextField","onChange","target","helperText","FormGroup","FormControlLabel","control","Checkbox","checked","event","label","color","DialogActions","Button","onClick","trackId","Date","now","session","getSession","assemblyManager","assemblyName","assemblyNames","isSessionWithAddTracks","addTrackConf","name","type","adapter","search","sequenceAdapter","getSnapshot","get","configuration","sequence","showTrack","variant"],"sourceRoot":""}
\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/static/js/1304.a512b560.chunk.js
--- a/x/static/js/1304.a512b560.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/1304.a512b560.chunk.js.map
--- a/x/static/js/1304.a512b560.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/1310.8a044016.chunk.js
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/1326.19289940.chunk.js
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/1326.19289940.chunk.js.map
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/1345.aaaaf175.chunk.js
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/1345.aaaaf175.chunk.js.map
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/1354.ded982ce.chunk.js
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/14.b9913d1d.chunk.js
--- a/x/static/js/14.b9913d1d.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/14.b9913d1d.chunk.js.map
--- a/x/static/js/14.b9913d1d.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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i < lines.length; i++) {\\n const line = lines[i]!\\n const cols = line.split(\'\\\\t\')\\n const r1 = cols[0]!\\n const r2 = cols[3]!\\n if (!feats1[r1]) {\\n feats1[r1] = []\\n }\\n if (!feats2[r2]) {\\n feats2[r2] = []\\n }\\n feats1[r1].push(line)\\n feats2[r2].push(line)\\n }\\n const columnNames = this.getConf(\'columnNames\')\\n\\n return {\\n header,\\n feats1,\\n feats2,\\n columnNames,\\n }\\n }\\n\\n private async loadData(opts: BaseOptions = {}) {\\n if (!this.bedpeFeatures) {\\n this.bedpeFeatures = this.loadDataP(opts).catch((e: unknown) => {\\n this.bedpeFeatures = undefined\\n throw e\\n })\\n }\\n\\n return this.bedpeFeatures\\n }\\n\\n public async getRefNames(opts: BaseOptions = {}) {\\n const { feats1, feats2 } = await this.loadData(opts)\\n return [...new Set([...Object.keys(feats1), ...Object.keys(feats2)])]\\n }\\n\\n async getHeader(opts: BaseOptions = {}) {\\n const { header } = await this.loadData(opts)\\n return header\\n }\\n\\n async getNames() {\\n const { header, columnNames } = await this.loadData()\\n if (columnNames.length) {\\n return columnNames\\n }\\n const defs = header.split(/\\\\n|\\\\r\\\\n|\\\\r/).filter(f => !!f)\\n const defline = defs.at(-1)\\n return defline?.includes(\'\\\\t\')\\n ? defline\\n .slice(1)\\n .split(\'\\\\t\')\\n .map(field => field.trim())\\n : undefined\\n }\\n\\n private async loadFeatureTreeP(refName: string) {\\n const { feats1, feats2 } = await this.loadData()\\n const names = await this.getNames()\\n const intervalTree = new IntervalTree()\\n const ret1 =\\n feats1[refName]?.map((f, i) =>\\n featureData(f, `${this.id}-${refName}-${i}-r1`, false, names),\\n ) ?? []\\n const ret2 =\\n feats2[refName]?.map((f, i) =>\\n featureData(f, `${this.id}-${refName}-${i}-r2`, true, names),\\n ) ?? []\\n\\n for (const obj of [...ret1, ...ret2]) {\\n intervalTree.insert([obj.get(\'start\'), obj.get(\'end\')], obj)\\n }\\n\\n return intervalTree\\n }\\n\\n private async loadFeatureTree(refName: string) {\\n if (!this.intervalTrees[refName]) {\\n this.intervalTrees[refName] = this.loadFeatureTreeP(refName).catch(\\n (e: unknown) => {\\n this.intervalTrees[refName] = undefined\\n throw e\\n },\\n )\\n }\\n return this.intervalTrees[refName]\\n }\\n\\n public getFeatures(query: Region, opts: BaseOptions = {}) {\\n return ObservableCreate<Feature>(async observer => {\\n const { start, end, refName } = query\\n const intervalTree = await this.loadFeatureTree(refName)\\n intervalTree?.search([start, end]).forEach(f => {\\n observer.next(f)\\n })\\n observer.complete()\\n }, opts.signal)\\n }\\n\\n public freeResources(): void {}\\n}\\n"],"names":["svTypes","Set","featureData","line","uniqueId","flip","names","l","split","ref1","start1","end1","ref2","start2","end2","name","score","strand1","parseStrand","strand2","extra","slice","rest","Object","fromEntries","map","n","idx","ALT","has","undefined","SimpleFeature","start","end","type","refName","strand","mate","BedpeAdapter","BaseFeatureDataAdapter","intervalTrees","loadDataP","opts","pm","this","pluginManager","bedLoc","getConf","buf","openLocation","readFile","buffer","isGzip","unzip","length","Error","lines","TextDecoder","fatal","decode","filter","f","headerLines","i","startsWith","push","header","join","feats1","feats2","cols","r1","r2","columnNames","loadData","bedpeFeatures","catch","e","getRefNames","keys","getHeader","getNames","defline","at","includes","field","trim","loadFeatureTreeP","intervalTree","IntervalTree","ret1","id","ret2","obj","insert","get","loadFeatureTree","getFeatures","query","ObservableCreate","async","search","forEach","observer","next","complete","signal","freeResources"],"sourceRoot":""}\n\\ No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/1503.cc48d25a.chunk.js
--- a/x/static/js/1503.cc48d25a.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,2 +0,0 @@\n-"use strict";(globalThis.webpackChunk_jbrowse_web=globalThis.webpackChunk_jbrowse_web||[]).push([[1503],{61503:(e,t,r)=>{r.r(t),r.d(t,{default:()=>y});var n=r(46377),s=r(99834),a=r(66885),i=r(32598),o=r(99546),c=r(7706);const l=["seq_name","source","featureType","start","end","score","strand","frame","attributes"];function u(e){return null===e?null:String(e).replace(/%([0-9A-Fa-f]{2})/g,((e,t)=>String.fromCharCode(parseInt(t,16))))}function f(e,t){return String(t).replace(e,(e=>{let t=e.charCodeAt(0).toString(16).toUpperCase();return t.length<2&&(t=`0${t}`),`%${t}`}))}function h(e){return f(/[\\n;\\r\\t=%&,\\x00-\\x1f\\x7f-\\xff]/g,e)}const d=["-",".","+"];function p(e,t){const r=null===e.attributes||void 0===e.attributes?".":function(e){const t=[];return Object.keys(e).forEach((r=>{const n=e[r];let s;s=n.hasOwnProperty("toString")?h(n.toString()):Array.isArray(n.values)?n.values.map(h).join(","):Array.isArray(n)?n.map(h).join(","):h(n),t.push(`${h(r)} ${s}`)})),t.length?t.join("; ").concat(";"):"."}(e.attributes),n=[];for(let t=0;t<8;t+=1){const r=e[l[t]];n[t]=6===t?null==r?".":d[r+1]||r:null==r?".":f(/[\\n\\r\\t%\\x00-\\x1f\\x7f-\\xff]/g,String(r))}n[8]=r;const s=`${n.join("\\t")}\\n`;return t[s]?"":(t[s]=!0,s)}function m(e,t){if(Array.isArray(e))return e.map((e=>m(e,t))).join("");const r=[p(e,t)];return["child_features","derived_features"].forEach((n=>{e[n]&&r.push(...e[n].map((e=>m(e,t))))})),r.join("")}function _(e){return m(e,{})}const b={Parent:"child_features",Derives_from:"derived_features"};class v{constructor(e){const t=()=>{};Object.assign(this,{featureCallback:e.featureCallback||t,endCallback:e.endCallback||t,commentCallback:e.commentCallback||t,errorCallback:e.errorCallback||t,directiveCallback:e.directiveCallback||t,sequenceCallback:e.sequenceCallback||t,bufferSize:void 0===e.bufferSize?1e3:e.bufferSize,_underConstructionTopLevel:[],_underConstructionById:{},_completedReferences:{},_underConstructionOrphans:{},eof:!1,lineNumber:0})}addLine(e){if(this.eof)return;if(this.lineNumber+=1,/^\\s*[^#\\s>]/.test(e))return void this._bufferLine(e);const t=/^\\s*(#+)(.*)/.exec(e);if(t){let[,r,n]=t;if(3===r.length)this._emitAllUnderConstructionFeatures();else if(2===r.length){const t=function(e){const t=/^\\s*##\\s*(\\S+)\\s*(.*)/.exec(e);if(!t)return null;const r=t[1];let n=t[2];const s={directive:r};if(n.length&&(n=n.replace(/\\r?\\n$/,""),s.value=n),"sequence-region"===r){const[e,t,r]=n.split(/\\s+/,3);s.seq_id=e,s.start=t&&t.replace(/\\D/g,""),s.end=r&&r.replace(/\\D/g,"")}else if("genome-build"===r){const[e,t]=n.split(/\\s+/,2);s.source=e,s.buildname=t}return s}(e);this._emitItem(t)}else n=n.replace(/\\s*/,""),this._emitItem({comment:n})}else if(!/^\\s*$/.test(e)){const t=e.replace(/\\r?\\n?$/g,"");throw new Error(`GTF parse error. Cannot parse \'${t}\'.`)}}_emitItem(e){e[0]?this.featureCallback(e):e.directive?this.directiveCallback(e):e.comment&&this.commentCallback(e)}finish(){this._emitAllUnderConstructionFeatures(),this.endCallback()}_enforceBufferSizeLimit(e=0){const t=e=>{var r,n,s;(null===(s=null===(n=null===(r=null==e?void 0:e[0])||void 0===r?void 0:r.attributes)||void 0===n?void 0:n.ID)||void 0===s?void 0:s[0])&&(e[0].attributes.ID.forEach((e=>{delete this._underConstructionById[e],delete this._completedReferences[e]})),e.forEach((e=>{e.child_features&&e.child_features.forEach((e=>{t(e)})),e.derived_features&&e.derived_features.forEach((e=>{t(e)}))})))};for(;this._underConstructionTopLevel.length+e>this.bufferSize;){const e=this._underConstructionTopLevel.shift();this._emitItem(e),t(e)}}_emitAllUnderConstructionFeatures(){if(this._underConstructionTopLevel.forEach(this._emitItem.bind(this)),this._underConstructionTopLevel=[],this._underConstructionById={},this._completedReferences={},Object.values(this._underConstructionOrphans).filter((e=>Object.keys(e).length)).length)throw new Error(`some features reference other features that do not exist in the file (or in the same \'###\' scope). ${JSON.stringify(this._underConstructionOr'..b'o=[t],this._enforceBufferSizeLimit(1),a.length||i.length||this._underConstructionTopLevel.push(o),this._underConstructionById[e]=o,this._resolveReferencesTo(o,e))})),this._resolveReferencesFrom(o||[t],{Parent:a,Derives_from:i},s)}_resolveReferencesTo(e,t){const r=this._underConstructionOrphans[t];r&&Object.keys(r).forEach((t=>{const n=b[t]||t.toLowerCase();e.forEach((e=>{e[n].push(...r[t]),delete r[t]}))}))}_parseError(e){this.eof=!0,this.errorCallback(`${this.lineNumber}: ${e}`)}_resolveReferencesFrom(e,t,r){Object.entries(t).forEach((([t,n])=>{let s;n.forEach((n=>{const a=this._underConstructionById[n];var i,o;a?(o=e,(i=a)[0].start=Math.min(i[0].start,o[0].start),i[0].end=Math.max(i[0].end,o[0].end),s||(s=b[t]||t.toLowerCase()),r.filter((e=>function(e,t,r){let n=e[t];n||(n={},e[t]=n);const s=n[r]||!1;return n[r]=!0,s}(this._completedReferences,e,`${t},${n}`))).length||a.forEach((t=>{t[s].push(e)}))):(this._underConstructionOrphans[n]||(this._underConstructionOrphans[n]={}),this._underConstructionOrphans[n][t]||(this._underConstructionOrphans[n][t]=[]),this._underConstructionOrphans[n][t].push(e))}))}))}}function g(e){const t={...e};t.start-=1,t.strand={"+":1,"-":-1,".":0,"?":void 0}[e.strand],t.phase=Number(e.frame),t.refName=e.seq_name,null===e.score&&(t.score=void 0),null===e.frame&&(t.score=void 0);const r=new Set(["start","end","seq_name","score","featureType","source","frame","strand"]);for(const n of Object.keys(e.attributes)){let s=n.toLowerCase();if(r.has(s)&&(s+="2"),e.attributes[n]){let r=e.attributes[n];Array.isArray(r)&&1===r.length&&(r=r[0].replaceAll(/^"|"$/g,"")),t[s]=r}}return t.refName=t.seq_name,t.type=t.featureType,e.child_features&&e.child_features.length>0&&(t.subfeatures=e.child_features.flatMap((e=>e.map((e=>g(e)))))),t.child_features=void 0,t.data=void 0,t.derived_features=void 0,t._linehash=void 0,t.attributes=void 0,t.seq_name=void 0,t.featureType=void 0,t.frame=void 0,t.transcript_id&&(t.name=t.transcript_id),t}const C="undefined"!=typeof TextDecoder?new TextDecoder("utf8"):void 0;class y extends n.BaseFeatureDataAdapter{calculatedIntervalTreeMap={};async loadDataP(e){const{statusCallback:t=()=>{}}=e||{},r=await(0,s.openLocation)(this.getConf("gtfLocation"),this.pluginManager).readFile(e),n=(0,o.isGzip)(r)?await(0,o.updateStatus)("Unzipping",t,(()=>(0,c.unzip)(r))):r,a=[],l={};let u=0,f=0;for(;u<n.length;){const e=n.indexOf("\\n",u),r=-1===e?n.subarray(u):n.subarray(u,e),s=(C?.decode(r)||r.toString()).trim();if(s)if(s.startsWith("#"))a.push(s);else{if(s.startsWith(">"))break;{const e=s.indexOf("\\t"),t=s.slice(0,e);l[t]||(l[t]=""),l[t]+=`${s}\\n`}}f++%1e4==0&&t(`Loading ${Math.floor(u/1e6).toLocaleString("en-US")}/${Math.floor(n.length/1e6).toLocaleString("en-US")} MB`),u=e+1}const h=Object.fromEntries(Object.entries(l).map((([e,t])=>[e,r=>{if(!this.calculatedIntervalTreeMap[e]){r?.("Parsing GTF data");const n=new i.Ay;(function(e){if(!e)return[];const t=[],r=new v({featureCallback:e=>t.push(e),errorCallback:e=>{throw e}});for(const t of e.split(/\\r?\\n/))r.addLine(t);return r.finish(),t})(t).flat().map(((t,r)=>new o.SimpleFeature({data:g(t),id:`${this.id}-${e}-${r}`}))).forEach((e=>n.insert([e.get("start"),e.get("end")],e))),this.calculatedIntervalTreeMap[e]=n}return this.calculatedIntervalTreeMap[e]}])));return{header:a.join("\\n"),intervalTreeMap:h}}async loadData(e={}){return this.gtfFeatures||(this.gtfFeatures=this.loadDataP(e).catch((e=>{throw this.gtfFeatures=void 0,e}))),this.gtfFeatures}async getRefNames(e={}){const{intervalTreeMap:t}=await this.loadData(e);return Object.keys(t)}async getHeader(e={}){const{header:t}=await this.loadData(e);return t}getFeatures(e,t={}){return(0,a.ObservableCreate)((async r=>{try{const{start:n,end:s,refName:a}=e,{intervalTreeMap:i}=await this.loadData(t);i[a]?.(t.statusCallback).search([n,s]).forEach((e=>{r.next(e)})),r.complete()}catch(e){r.error(e)}}),t.signal)}freeResources(){}}}}]);\n-//# sourceMappingURL=1503.cc48d25a.chunk.js.map\n\\ No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/1503.cc48d25a.chunk.js.map
--- a/x/static/js/1503.cc48d25a.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/1516.ca4ab8f0.chunk.js
--- a/x/static/js/1516.ca4ab8f0.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/1516.ca4ab8f0.chunk.js.map
--- a/x/static/js/1516.ca4ab8f0.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/1537.4fdb4e95.chunk.js
--- a/x/static/js/1537.4fdb4e95.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/1537.4fdb4e95.chunk.js.map
--- a/x/static/js/1537.4fdb4e95.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/1598.3b48685f.chunk.js
--- a/x/static/js/1598.3b48685f.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/1598.3b48685f.chunk.js.map
--- a/x/static/js/1598.3b48685f.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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--- a/x/static/js/1637.21a8cf01.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/1725.795fc4d3.chunk.js
--- a/x/static/js/1725.795fc4d3.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/1752.a727a500.chunk.js
--- a/x/static/js/1752.a727a500.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/1752.a727a500.chunk.js.map
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/1757.a6d05bc3.chunk.js
--- a/x/static/js/1757.a6d05bc3.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/1811.7cfd8419.chunk.js
--- a/x/static/js/1811.7cfd8419.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/1811.7cfd8419.chunk.js.map
--- a/x/static/js/1811.7cfd8419.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/static/js/1822.2cbe112a.chunk.js
--- a/x/static/js/1822.2cbe112a.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/1822.2cbe112a.chunk.js.map
--- a/x/static/js/1822.2cbe112a.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/1824.c2ed4bca.chunk.js
--- a/x/static/js/1824.c2ed4bca.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/1999.2554e815.chunk.js
--- a/x/static/js/1999.2554e815.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/2018.9ce7fb06.chunk.js
--- a/x/static/js/2018.9ce7fb06.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/2018.9ce7fb06.chunk.js.map
--- a/x/static/js/2018.9ce7fb06.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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'' : '-sessionTrack',\n ].join('')\n\n // allow list of bigwigs in JSON format or line-by-line\n let bigWigs: unknown[]\n try {\n bigWigs = JSON.parse(val)\n } catch (e) {\n bigWigs = val\n .split(/\\n|\\r\\n|\\r/)\n .map(f => f.trim())\n .filter(f => !!f)\n }\n const obj =\n typeof bigWigs[0] === 'string'\n ? { bigWigs }\n : { subadapters: bigWigs }\n\n if (isSessionWithAddTracks(session)) {\n session.addTrackConf({\n trackId,\n type: 'MultiQuantitativeTrack',\n name: trackName,\n assemblyNames: [model.assembly],\n adapter: {\n type: 'MultiWiggleAdapter',\n ...obj,\n },\n })\n\n model.view?.showTrack(trackId)\n }\n model.clearData()\n if (isSessionModelWithWidgets(session)) {\n session.hideWidget(model)\n }\n }}\n >\n Submit\n </Button>\n\n <p>Additional notes: </p>\n <ul>\n <li>\n The list of bigwig files in the text box can be a list of URLs, or a\n list of elements like{' '}\n <code>{`[{\"type\":\"BigWigAdapter\",\"bigWigLocation\":{\"uri\":\"http://host/file.bw\"}, \"color\":\"green\",\"source\":\"name for subtrack\"}]`}</code>{' '}\n to apply e.g. the color attribute to the view\n </li>\n <li>\n Adding local files will update the textbox with JSON contents that are\n ready to submit with the \"Submit\" button\n </li>\n </ul>\n </Paper>\n )\n}\n"],"names":["useStyles","makeStyles","theme","textbox","width","paper","margin","spacing","padding","submit","marginTop","marginBottom","display","MultiWiggleWidget","model","classes","val","setVal","useState","trackName","setTrackName","Date","now","React","Paper","className","TextField","multiline","rows","value","onChange","event","target","placeholder","variant","Button","component","type","hidden","multiple","res","files","map","file","bigWigLocation","isElectron","localPath","path","locationType","storeBlobLocation","blob","source","name","JSON","stringify","helperText","onClick","session","getSession","trackId","toLowerCase","replaceAll","adminMode","join","bigWigs","parse","e","split","f","trim","filter","obj","subadapters","isSessionWithAddTracks","addTrackConf","assemblyNames","assembly","adapter","view","showTrack","clearData","isSessionModelWithWidgets","hideWidget"],"sourceRoot":""}
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/2047.b1e80504.chunk.js
--- a/x/static/js/2047.b1e80504.chunk.js Fri Oct 18 11:57:55 2024 +0000
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CardMedia.propTypes /* remove-proptypes */ = {\n // ┌────────────────────────────── Warning ──────────────────────────────┐\n // │ These PropTypes are generated from the TypeScript type definitions. │\n // │ To update them, edit the d.ts file and run `pnpm proptypes`. │\n // └─────────────────────────────────────────────────────────────────────┘\n /**\n * The content of the component.\n */\n children: chainPropTypes(PropTypes.node, props => {\n if (!props.children && !props.image && !props.src && !props.component) {\n return new Error('MUI: Either `children`, `image`, `src` or `component` prop must be specified.');\n }\n return null;\n }),\n /**\n * Override or extend the styles applied to the component.\n */\n classes: PropTypes.object,\n /**\n * @ignore\n */\n className: PropTypes.string,\n /**\n * The component used for the root node.\n * Either a string to use a HTML element or a component.\n */\n component: PropTypes.elementType,\n /**\n * Image to be displayed as a background image.\n * Either `image` or `src` prop must be specified.\n * Note that caller must specify height otherwise the image will not be visible.\n */\n image: PropTypes.string,\n /**\n * An alias for `image` property.\n * Available only with media components.\n * Media components: `video`, `audio`, `picture`, `iframe`, `img`.\n */\n src: PropTypes.string,\n /**\n * @ignore\n */\n style: PropTypes.object,\n /**\n * The system prop that allows defining system overrides as well as additional CSS styles.\n */\n sx: PropTypes.oneOfType([PropTypes.arrayOf(PropTypes.oneOfType([PropTypes.func, PropTypes.object, PropTypes.bool])), PropTypes.func, PropTypes.object])\n} : void 0;\nexport default CardMedia;","import generateUtilityClasses from '@mui/utils/generateUtilityClasses';\nimport generateUtilityClass from '@mui/utils/generateUtilityClass';\nexport function getCardMediaUtilityClass(slot) {\n return generateUtilityClass('MuiCardMedia', slot);\n}\nconst cardMediaClasses = generateUtilityClasses('MuiCardMedia', ['root', 'media', 'img']);\nexport default cardMediaClasses;"],"names":["CardMediaRoot","name","slot","overridesResolver","props","styles","ownerState","isMediaComponent","isImageComponent","root","media","img","display","backgroundSize","backgroundRepeat","backgroundPosition","variants","style","width","objectFit","MEDIA_COMPONENTS","IMAGE_COMPONENTS","inProps","ref","children","className","component","image","src","other","includes","composedStyle","backgroundImage","classes","slots","useUtilityClasses","as","role","undefined","getCardMediaUtilityClass"],"sourceRoot":""}
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/2189.3c65daf8.chunk.js.map
--- a/x/static/js/2189.3c65daf8.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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--- a/x/static/js/2197.a5134ce4.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/2241.3d359b22.chunk.js.map
--- a/x/static/js/2241.3d359b22.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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internal component.\\n */\\nimport { jsx as _jsx } from \\"react/jsx-runtime\\";\\nexport default createSvgIcon(/*#__PURE__*/_jsx(\\"path\\", {\\n d: \\"M12 0a12 12 0 1 0 0 24 12 12 0 0 0 0-24zm-2 17l-5-5 1.4-1.4 3.6 3.6 7.6-7.6L19 8l-9 9z\\"\\n}), \'CheckCircle\');","\'use client\';\\n\\nimport * as React from \'react\';\\nimport createSvgIcon from \\"../../utils/createSvgIcon.js\\";\\n\\n/**\\n * @ignore - internal component.\\n */\\nimport { jsx as _jsx } from \\"react/jsx-runtime\\";\\nexport default createSvgIcon(/*#__PURE__*/_jsx(\\"path\\", {\\n d: \\"M1 21h22L12 2 1 21zm12-3h-2v-2h2v2zm0-4h-2v-4h2v4z\\"\\n}), \'Warning\');","\'use client\';\\n\\nvar _circle;\\nimport * as React from \'react\';\\nimport PropTypes from \'prop-types\';\\nimport clsx from \'clsx\';\\nimport composeClasses from \'@mui/utils/composeClasses\';\\nimport { styled } from \\"../zero-styled/index.js\\";\\nimport memoTheme from \\"../utils/memoTheme.js\\";\\nimport { useDefaultProps } from \\"../DefaultPropsProvider/index.js\\";\\nimport CheckCircle from \\"../internal/svg-icons/CheckCircle.js\\";\\nimport Warning from \\"../internal/svg-icons/Warning.js\\";\\nimport SvgIcon from \\"../SvgIcon/index.js\\";\\nimport stepIconClasses, { getStepIconUtilityClass } from \\"./stepIconClasses.js\\";\\nimport { jsx as _jsx, jsxs as _jsxs } from \\"react/jsx-runtime\\";\\nconst useUtilityClasses = ownerState => {\\n const {\\n classes,\\n active,\\n completed,\\n error\\n } = ownerState;\\n const slots = {\\n root: [\'root\', active && \'active\', completed && \'completed\', error && \'error\'],\\n text: [\'text\']\\n };\\n return composeClasses(slots, getStepIconUt'..b'n completed = false,\\n error = false,\\n icon,\\n ...other\\n } = props;\\n const ownerState = {\\n ...props,\\n active,\\n completed,\\n error\\n };\\n const classes = useUtilityClasses(ownerState);\\n if (typeof icon === \'number\' || typeof icon === \'string\') {\\n const className = clsx(classNameProp, classes.root);\\n if (error) {\\n return /*#__PURE__*/_jsx(StepIconRoot, {\\n as: Warning,\\n className: className,\\n ref: ref,\\n ownerState: ownerState,\\n ...other\\n });\\n }\\n if (completed) {\\n return /*#__PURE__*/_jsx(StepIconRoot, {\\n as: CheckCircle,\\n className: className,\\n ref: ref,\\n ownerState: ownerState,\\n ...other\\n });\\n }\\n return /*#__PURE__*/_jsxs(StepIconRoot, {\\n className: className,\\n ref: ref,\\n ownerState: ownerState,\\n ...other,\\n children: [_circle || (_circle = /*#__PURE__*/_jsx(\\"circle\\", {\\n cx: \\"12\\",\\n cy: \\"12\\",\\n r: \\"12\\"\\n })), /*#__PURE__*/_jsx(StepIconText, {\\n className: classes.text,\\n x: \\"12\\",\\n y: \\"12\\",\\n textAnchor: \\"middle\\",\\n dominantBaseline: \\"central\\",\\n ownerState: ownerState,\\n children: icon\\n })]\\n });\\n }\\n return icon;\\n});\\nprocess.env.NODE_ENV !== \\"production\\" ? 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diff -r cec274db51c0 -r ed3a21033188 x/static/js/2249.b91f0bb3.chunk.js
--- a/x/static/js/2249.b91f0bb3.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/2249.b91f0bb3.chunk.js.map
--- a/x/static/js/2249.b91f0bb3.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/2306.f8d640f4.chunk.js
--- a/x/static/js/2306.f8d640f4.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/2306.f8d640f4.chunk.js.map
--- a/x/static/js/2306.f8d640f4.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/2321.ef211da9.chunk.js
--- a/x/static/js/2321.ef211da9.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/2424.7cd6703f.chunk.js
--- a/x/static/js/2424.7cd6703f.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/2424.7cd6703f.chunk.js.map
--- a/x/static/js/2424.7cd6703f.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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(\n <BlockMsg\n message={`${error}`}\n severity=\"error\"\n action={\n <Tooltip title=\"Reload\">\n <Button\n data-testid=\"reload_button\"\n onClick={() => {\n model.reload()\n }}\n >\n Reload\n </Button>\n </Tooltip>\n }\n />\n ) : regionTooLarge ? (\n model.regionCannotBeRendered()\n ) : (\n <DataDisplay model={model}>{children}</DataDisplay>\n )\n})\n\nconst DataDisplay = observer(function ({\n model,\n children,\n}: {\n model: LinearReadArcsDisplayModel | LinearReadCloudDisplayModel\n children?: React.ReactNode\n}) {\n const { drawn, loading } = model\n const view = getContainingView(model) as LinearGenomeViewModel\n const left = (model.lastDrawnOffsetPx || 0) - view.offsetPx\n return (\n // this data-testid is located here because changing props on the canvas\n // itself is very sensitive to triggering ref invalidation\n <div data-testid={`drawn-${drawn}`}>\n <div style={{ position: 'absolute', left }}>{children}</div>\n {left !== 0 || loading ? <LoadingBar model={model} /> : null}\n </div>\n )\n})\n\nconst LoadingBar = observer(function ({\n model,\n}: {\n model: LinearReadArcsDisplayModel | LinearReadCloudDisplayModel\n}) {\n const { classes } = useStyles()\n const { message } = model\n return (\n <div className={classes.loading}>\n <LoadingEllipses message={message} />\n </div>\n )\n})\n\nexport default BaseDisplayComponent\n"],"names":["Arcs","observer","model","view","getContainingView","width","Math","round","dynamicBlocks","totalWidthPx","height","cb","useCallback","ref","setRef","React","style","position","BaseDisplayComponent","useStyles","makeStyles","theme","loading","backgroundColor","palette","background","default","backgroundImage","action","disabledBackground","bottom","right","pointerEvents","textAlign","children","error","regionTooLarge","BlockMsg","message","severity","Tooltip","title","Button","onClick","reload","regionCannotBeRendered","DataDisplay","drawn","left","lastDrawnOffsetPx","offsetPx","LoadingBar","classes","className","LoadingEllipses"],"sourceRoot":""}
\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/static/js/246.9848bd41.chunk.js
--- a/x/static/js/246.9848bd41.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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flex item properties to be used to lay out the children.\\n */\\n children: PropTypes.node,\\n /**\\n * Override or extend the styles applied to the component.\\n */\\n classes: PropTypes.object,\\n /**\\n * @ignore\\n */\\n className: PropTypes.string,\\n /**\\n * The component used for the root node.\\n * Either a string to use a HTML element or a component.\\n */\\n component: PropTypes.elementType,\\n /**\\n * If `true`, disables gutter padding.\\n * @default false\\n */\\n disableGutters: PropTypes.bool,\\n /**\\n * The system prop that allows defining system overrides as well as additional CSS styles.\\n */\\n sx: PropTypes.oneOfType([PropTypes.arrayOf(PropTypes.oneOfType([PropTypes.func, PropTypes.object, PropTypes.bool])), PropTypes.func, PropTypes.object]),\\n /**\\n * The variant to use.\\n * @default \'regular\'\\n */\\n variant: PropTypes /* @typescript-to-proptypes-ignore */.oneOfType([PropTypes.oneOf([\'dense\', \'regular\']), PropTypes.string])\\n} : void 0;\\nexport default Toolbar;","import generateUtilityClasses from \'@mui/utils/generateUtilityClasses\';\\nimport generateUtilityClass from \'@mui/utils/generateUtilityClass\';\\nexport function getToolbarUtilityClass(slot) {\\n return generateUtilityClass(\'MuiToolbar\', slot);\\n}\\nconst toolbarClasses = generateUtilityClasses(\'MuiToolbar\', [\'root\', \'gutters\', \'regular\', \'dense\']);\\nexport default 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diff -r cec274db51c0 -r ed3a21033188 x/static/js/2493.20e8e76c.chunk.js
--- a/x/static/js/2493.20e8e76c.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/2583.db78b17f.chunk.js
--- a/x/static/js/2583.db78b17f.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/26.604133d9.chunk.js
--- a/x/static/js/26.604133d9.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/2627.300bea43.chunk.js
--- a/x/static/js/2627.300bea43.chunk.js Fri Oct 18 11:57:55 2024 +0000
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flex item properties to be used to lay out the children.\\n */\\n children: PropTypes.node,\\n /**\\n * Override or extend the styles applied to the component.\\n */\\n classes: PropTypes.object,\\n /**\\n * @ignore\\n */\\n className: PropTypes.string,\\n /**\\n * The component used for the root node.\\n * Either a string to use a HTML element or a component.\\n */\\n component: PropTypes.elementType,\\n /**\\n * If `true`, disables gutter padding.\\n * @default false\\n */\\n disableGutters: PropTypes.bool,\\n /**\\n * The system prop that allows defining system overrides as well as additional CSS styles.\\n */\\n sx: PropTypes.oneOfType([PropTypes.arrayOf(PropTypes.oneOfType([PropTypes.func, PropTypes.object, PropTypes.bool])), PropTypes.func, PropTypes.object]),\\n /**\\n * The variant to use.\\n * @default \'regular\'\\n */\\n variant: PropTypes /* @typescript-to-proptypes-ignore */.oneOfType([PropTypes.oneOf([\'dense\', \'regular\']), PropTypes.string])\\n} : void 0;\\nexport default Toolbar;","import generateUtilityClasses from \'@mui/utils/generateUtilityClasses\';\\nimport generateUtilityClass from \'@mui/utils/generateUtilityClass\';\\nexport function getToolbarUtilityClass(slot) {\\n return generateUtilityClass(\'MuiToolbar\', slot);\\n}\\nconst toolbarClasses = generateUtilityClasses(\'MuiToolbar\', [\'root\', \'gutters\', \'regular\', \'dense\']);\\nexport default toolbarClasses;"],"names":["circularRotateKeyframe","circularDashKeyframe","rotateAnimation","dashAnimation","CircularProgressRoot","name","slot","overridesResolver","props","styles","ownerState","root","variant","color","theme","display","variants","style","transition","transitions","create","animation","Object","entries","palette","filter","map","vars","main","CircularProgressSVG","svg","CircularProgressCircle","circle","disableShrink","circleDisableShrink","stroke","strokeDasharray","strokeDashoffset","inProps","ref","className","size","thickness","value","other","classes","slots","useUtilityClasses","circleStyle","rootStyle","rootProps","circumference","Math","PI","toFixed","round","transform","width","height","role","children","viewBox","cx","cy","r","fill","strokeWidth","getCircularProgressUtilityClass","mapEventPropToEvent","eventProp","substring","toLowerCase","ClickAwayListener","disableReactTree","mouseEvent","onClickAway","touchEvent","movedRef","nodeRef","activatedRef","syntheticEventRef","setTimeout","current","handleRef","handleClickAway","event","insideReactTree","doc","documentElement","clientWidth","clientX","clientHeight","clientY","clickedRootScrollbar","insideDOM","composedPath","includes","contains","target","createHandleSynthetic","handlerName","childrenPropsHandler","childrenProps","mappedTouchEvent","handleTouchMove","addEventListener","removeEventListener","mappedMouseEvent","ToolbarRoot","disableGutters","gutters","position","alignItems","paddingLeft","spacing","paddingRight","breakpoints","up","minHeight","mixins","toolbar","component","as","getToolbarUtilityClass"],"sourceRoot":""}\n\\ No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/2645.4b79a04c.chunk.js
--- a/x/static/js/2645.4b79a04c.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/2645.4b79a04c.chunk.js.map
--- a/x/static/js/2645.4b79a04c.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/266.94eb2bf9.chunk.js
--- a/x/static/js/266.94eb2bf9.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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Lowercase<EventName> : never` once generatePropTypes runs with TS 4.1\\nimport { jsx as _jsx } from \\"react/jsx-runtime\\";\\nfunction mapEventPropToEvent(eventProp) {\\n return eventProp.substring(2).toLowerCase();\\n}\\nfunction clickedRootScrollbar(event, doc) {\\n return doc.documentElement.clientWidth < event.clientX || doc.documentElement.clientHeight < event.clientY;\\n}\\n/**\\n * Listen for click events that occur somewhere in the document, outside of the element itself.\\n * For instance, if you need to hide a menu when people click anywhere else on your page.\\n *\\n * Demos:\\n *\\n * - [Click-Away Listener](https://mui.com/material-ui/react-click-away-listener/)\\n * - [Menu](https://mui.com/material-ui/react-menu/)\\n *\\n * API:\\n *\\n * - [ClickAwayListener API](https://mui.com/material-ui/api/click-away-listener/)\\n */\\nfunction ClickAwayListener(props) {\\n const {\\n children,\\n disableReactTree = false,\\n mouseEvent = \'onClick\',\\n onClickAway,\\n touchEvent = \'onTouchEnd\'\\n } = props;\\n const movedRef = React.useRef(false);\\n const nodeRef = React.useRef(null);\\n const activatedRef = React.useRef(false);\\n const syntheticEventRef = React.useRef(false);\\n React.useEffect(() => {\\n // Ensure that this component is not \\"activated\\" synchronously.\\n // https://github.com/facebook/react/issues/20074\\n setTimeout(() => {\\n activatedRef.current = true;\\n }, 0);\\n return () => {\\n activatedRef.current = false;\\n };\\n }, []);\\n const handleRef = useForkRef(getReactNodeRef(children), nodeRef);\\n\\n // The handler doesn\'t take event.defaultPrevented into account:\\n //\\n // event.preventDefault() is meant to stop default behaviors like\\n // clicking a checkbox to check it, hitting a button to submit a form,\\n // and hitting left arrow to move the cursor in a text input etc.\\n /'..b'urrent = true;\\n const childrenPropsHandler = children.props[handlerName];\\n if (childrenPropsHandler) {\\n childrenPropsHandler(event);\\n }\\n };\\n const childrenProps = {\\n ref: handleRef\\n };\\n if (touchEvent !== false) {\\n childrenProps[touchEvent] = createHandleSynthetic(touchEvent);\\n }\\n React.useEffect(() => {\\n if (touchEvent !== false) {\\n const mappedTouchEvent = mapEventPropToEvent(touchEvent);\\n const doc = ownerDocument(nodeRef.current);\\n const handleTouchMove = () => {\\n movedRef.current = true;\\n };\\n doc.addEventListener(mappedTouchEvent, handleClickAway);\\n doc.addEventListener(\'touchmove\', handleTouchMove);\\n return () => {\\n doc.removeEventListener(mappedTouchEvent, handleClickAway);\\n doc.removeEventListener(\'touchmove\', handleTouchMove);\\n };\\n }\\n return undefined;\\n }, [handleClickAway, touchEvent]);\\n if (mouseEvent !== false) {\\n childrenProps[mouseEvent] = createHandleSynthetic(mouseEvent);\\n }\\n React.useEffect(() => {\\n if (mouseEvent !== false) {\\n const mappedMouseEvent = mapEventPropToEvent(mouseEvent);\\n const doc = ownerDocument(nodeRef.current);\\n doc.addEventListener(mappedMouseEvent, handleClickAway);\\n return () => {\\n doc.removeEventListener(mappedMouseEvent, handleClickAway);\\n };\\n }\\n return undefined;\\n }, [handleClickAway, mouseEvent]);\\n return /*#__PURE__*/_jsx(React.Fragment, {\\n children: /*#__PURE__*/React.cloneElement(children, childrenProps)\\n });\\n}\\nprocess.env.NODE_ENV !== \\"production\\" ? ClickAwayListener.propTypes /* remove-proptypes */ = {\\n // \xe2\x94\x8c\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80 Warning \xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x90\\n // \xe2\x94\x82 These PropTypes are generated from the TypeScript type definitions. \xe2\x94\x82\\n // \xe2\x94\x82 To update them, edit the TypeScript types and run `pnpm proptypes`. \xe2\x94\x82\\n // \xe2\x94\x94\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x98\\n /**\\n * The wrapped element.\\n */\\n children: elementAcceptingRef.isRequired,\\n /**\\n * If `true`, the React tree is ignored and only the DOM tree is considered.\\n * This prop changes how portaled elements are handled.\\n * @default false\\n */\\n disableReactTree: PropTypes.bool,\\n /**\\n * The mouse event to listen to. You can disable the listener by providing `false`.\\n * @default \'onClick\'\\n */\\n mouseEvent: PropTypes.oneOf([\'onClick\', \'onMouseDown\', \'onMouseUp\', \'onPointerDown\', \'onPointerUp\', false]),\\n /**\\n * Callback fired when a \\"click away\\" event is detected.\\n */\\n onClickAway: PropTypes.func.isRequired,\\n /**\\n * The touch event to listen to. You can disable the listener by providing `false`.\\n * @default \'onTouchEnd\'\\n */\\n touchEvent: PropTypes.oneOf([\'onTouchEnd\', \'onTouchStart\', false])\\n} : void 0;\\nif (process.env.NODE_ENV !== \'production\') {\\n // eslint-disable-next-line\\n ClickAwayListener[\'propTypes\' + \'\'] = exactProp(ClickAwayListener.propTypes);\\n}\\nexport { ClickAwayListener };"],"names":["mapEventPropToEvent","eventProp","substring","toLowerCase","ClickAwayListener","props","children","disableReactTree","mouseEvent","onClickAway","touchEvent","movedRef","nodeRef","activatedRef","syntheticEventRef","setTimeout","current","handleRef","handleClickAway","event","insideReactTree","doc","documentElement","clientWidth","clientX","clientHeight","clientY","clickedRootScrollbar","insideDOM","composedPath","includes","contains","target","createHandleSynthetic","handlerName","childrenPropsHandler","childrenProps","ref","mappedTouchEvent","handleTouchMove","addEventListener","removeEventListener","mappedMouseEvent"],"sourceRoot":""}\n\\ No newline at end of file\n'

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/2847.009c96ee.chunk.js.LICENSE.txt
--- a/x/static/js/2847.009c96ee.chunk.js.LICENSE.txt Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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- */

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--- a/x/static/js/2847.009c96ee.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/2861.aa6cd5b7.chunk.js
--- a/x/static/js/2861.aa6cd5b7.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/2872.5129bbd8.chunk.js
--- a/x/static/js/2872.5129bbd8.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/2885.8a30e856.chunk.js
--- a/x/static/js/2885.8a30e856.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/2885.8a30e856.chunk.js.map
--- a/x/static/js/2885.8a30e856.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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be unique within the page.\\n * Being unique within a form is insufficient since the `name` is used to generated IDs.\\n */\\n name: PropTypes.string,\\n /**\\n * Callback fired when the value changes.\\n * @param {React.SyntheticEvent} event The event source of the callback.\\n * @param {number|null} value The new value.\\n */\\n onChange: PropTypes.func,\\n /**\\n * Callback function that is fired when the hover state changes.\\n * @param {React.SyntheticEvent} event The event source of the callback.\\n * @param {number} value The new value.\\n */\\n onChangeActive: PropTypes.func,\\n /**\\n * @ignore\\n */\\n onMouseLeave: PropTypes.func,\\n /**\\n * @ignore\\n */\\n onMouseMove: PropTypes.func,\\n /**\\n * The minimum increment value change allowed.\\n * @default 1\\n */\\n precision: chainPropTypes(PropTypes.number, props => {\\n if (props.precision < 0.1) {\\n return new Error([\'MUI: The prop `precision` should be above 0.1.\', \'A value below this limit has an imperceptible 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Rating;"],"names":["createSvgIcon","d","getRatingUtilityClass","slot","generateUtilityClass","generateUtilityClasses","roundValueToPrecision","value","precision","nearest","Math","round","Number","toFixed","num","decimalPart","toString","split","length","getDecimalPrecision","RatingRoot","styled","name","overridesResolver","props","styles","ownerState","visuallyHidden","root","capitalize","size","readOnly","memoTheme","theme","display","position","fontSize","typography","pxToRem","color","cursor","textAlign","width","WebkitTapHighlightColor","disabled","opacity","vars","palette","action","disabledOpacity","pointerEvents","focusVisible","iconActive","outline","variants","style","RatingLabel","label","emptyValueFocused","labelEmptyValueActive","top","bottom","RatingIcon","icon","iconEmpty","iconFilled","iconHover","iconFocus","transition","transitions","create","duration","shortest","transform","RatingDecimal","shouldForwardProp","prop","slotShouldForwardProp","decimal","IconContainer","other","RatingItem","classes","emptyIcon","focus","getLabelText","highlightSelectedOnly","hover","IconContainerComponent","isActive","itemValue","labelProps","onBlur","onChange","onClick","onFocus","ratingValue","ratingValueRounded","isFilled","isHovered","isFocused","isChecked","id","useId","container","as","className","clsx","children","undefined","htmlFor","type","checked","defaultIcon","Star","defaultEmptyIcon","StarBorder","defaultLabelText","inProps","ref","defaultValue","emptyLabelText","max","nameProp","onChangeActive","onMouseLeave","onMouseMove","valueProp","valueDerived","setValueState","useControlled","controlled","default","valueRounded","isRtl","setState","setFocusVisible","rootRef","handleRef","useForkRef","handleChange","event","newValue","target","parseFloat","handleClear","clientX","clientY","handleFocus","isFocusVisible","newFocus","prev","handleBlur","setEmptyValueFocused","slots","labelEmptyValue","composeClasses","useUtilityClasses","rootNode","current","right","left","containerWidth","getBoundingClientRect","percent","newHover","clamp","role","Array","from","map","_","index","ratingItemProps","ceil","items","$","indexDecimal","itemDecimalValue","overflow"],"sourceRoot":""}\n\\ No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/2928.4ac8c386.chunk.js
--- a/x/static/js/2928.4ac8c386.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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-"use strict";(globalThis.webpackChunk_jbrowse_web=globalThis.webpackChunk_jbrowse_web||[]).push([[2928],{62928:(e,n,a)=>{a.r(n),a.d(n,{default:()=>u});var t=a(7552),l=a(29499),s=a(1343),c=a(29629),o=a(58507),r=a(5401),m=a(75785),h=a(49823);const i=(0,m.n9)()((()=>({container:{width:800}})));function u({handleClose:e,session:n}){const{classes:a}=i();return t.createElement(h.Dialog,{title:"Preferences",open:!0,onClose:e,maxWidth:"xl"},t.createElement(l.A,{className:a.container},t.createElement(s.A,{select:!0,label:"Theme",value:n.themeName,onChange:e=>{n.setThemeName(e.target.value)}},Object.entries(n.allThemes()).map((([e,n])=>t.createElement(c.A,{key:e,value:e},n.name||"(Unknown name)"))))),t.createElement(o.A,null,t.createElement(r.A,{onClick:e},"Close")))}}}]);
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/2928.4ac8c386.chunk.js.map
--- a/x/static/js/2928.4ac8c386.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/2968.4d90773a.chunk.js
--- a/x/static/js/2968.4d90773a.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/2968.4d90773a.chunk.js.map
--- a/x/static/js/2968.4d90773a.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/2977.aa562b03.chunk.js
--- a/x/static/js/2977.aa562b03.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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b'@@ -1,2 +0,0 @@\n-"use strict";(globalThis.webpackChunk_jbrowse_web=globalThis.webpackChunk_jbrowse_web||[]).push([[2977,7706],{47046:(e,t,a)=>{a.d(t,{A:()=>i});class r{}class n{constructor(){this.signals=new Set,this.abortController=new AbortController}addSignal(e=new r){if(this.signal.aborted)throw new Error("cannot add a signal, already aborted!");this.signals.add(e),e.aborted?this.handleAborted(e):"function"==typeof e.addEventListener&&e.addEventListener("abort",(()=>{this.handleAborted(e)}))}handleAborted(e){this.signals.delete(e),0===this.signals.size&&this.abortController.abort()}get signal(){return this.abortController.signal}abort(){this.abortController.abort()}}class s{constructor(){this.callbacks=new Set}addCallback(e=()=>{}){this.callbacks.add(e),e(this.currentMessage)}callback(e){this.currentMessage=e;for(const t of this.callbacks)t(e)}}class i{constructor({fill:e,cache:t}){if("function"!=typeof e)throw new TypeError("must pass a fill function");if("object"!=typeof t)throw new TypeError("must pass a cache object");if("function"!=typeof t.get||"function"!=typeof t.set||"function"!=typeof t.delete)throw new TypeError("cache must implement get(key), set(key, val), and and delete(key)");this.cache=t,this.fillCallback=e}static isAbortException(e){return"AbortError"===e.name||"ERR_ABORTED"===e.code||"AbortError: aborted"===e.message||"Error: aborted"===e.message}evict(e,t){this.cache.get(e)===t&&this.cache.delete(e)}fill(e,t,a,r){const i=new n,o=new s;o.addCallback(r);const l={aborter:i,promise:this.fillCallback(t,i.signal,(e=>{o.callback(e)})),settled:!1,statusReporter:o,get aborted(){return this.aborter.signal.aborted}};l.aborter.addSignal(a),l.aborter.signal.addEventListener("abort",(()=>{l.settled||this.evict(e,l)})),l.promise.then((()=>{l.settled=!0}),(()=>{l.settled=!0,this.evict(e,l)})).catch((e=>{throw console.error(e),e})),this.cache.set(e,l)}static checkSinglePromise(e,t){function a(){if(null==t?void 0:t.aborted)throw Object.assign(new 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diff -r cec274db51c0 -r ed3a21033188 x/static/js/2977.aa562b03.chunk.js.map
--- a/x/static/js/2977.aa562b03.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/2989.031b43a0.chunk.js
--- a/x/static/js/2989.031b43a0.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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--- a/x/static/js/3003.0f0cbacd.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3109.3173f682.chunk.js
--- a/x/static/js/3109.3173f682.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3109.3173f682.chunk.js.map
--- a/x/static/js/3109.3173f682.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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--- a/x/static/js/311.2c004784.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/311.2c004784.chunk.js.map
--- a/x/static/js/311.2c004784.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/3116.fa0100fd.chunk.js
--- a/x/static/js/3116.fa0100fd.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3116.fa0100fd.chunk.js.map
--- a/x/static/js/3116.fa0100fd.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/static/js/3120.3940249f.chunk.js
--- a/x/static/js/3120.3940249f.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3162.eb9bf76d.chunk.js.map
--- a/x/static/js/3162.eb9bf76d.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3167.312d0953.chunk.js
--- a/x/static/js/3167.312d0953.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3167.312d0953.chunk.js.map
--- a/x/static/js/3167.312d0953.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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-1 : 1,\\n extra: {\\n numMatches: +numMatches!,\\n blockLen: +blockLen!,\\n mappingQual: +mappingQual!,\\n ...rest,\\n },\\n } as PAFRecord\\n}\\n\\nexport function flipCigar(cigar: string[]) {\\n const arr = []\\n for (let i = cigar.length - 2; i >= 0; i -= 2) {\\n arr.push(cigar[i])\\n const op = cigar[i + 1]\\n if (op === \'D\') {\\n arr.push(\'I\')\\n } else if (op === \'I\') {\\n arr.push(\'D\')\\n } else {\\n arr.push(op)\\n }\\n }\\n return arr\\n}\\n\\nexport function swapIndelCigar(cigar: string) {\\n return cigar.replaceAll(\'D\', \'K\').replaceAll(\'I\', \'D\').replaceAll(\'K\', \'I\')\\n}\\n"],"names":["PAFAdapter","BaseFeatureDataAdapter","constructor","config","getSubAdapter","pluginManager","super","pifGzLoc","this","getConf","type","loc","pm","pif","TabixIndexedFile","filehandle","openLocation","csiFilehandle","undefined","tbiFilehandle","chunkCacheSize","getHeader","getAssemblyNames","assemblyNames","length","hasDataForRefName","getRefNames","opts","r1","regions","assemblyName","Error","idx","indexOf","names","getReferenceSequenceNames","filter","n","startsWith","map","slice","getFeatures","query","ObservableCreate","async","flip","letter","getLines","refName","start","end","lineCallback","line","fileOffset","r","parsePAFLine","qname","qstart","qend","mateName","tname","mateStart","tstart","mateEnd","tend","extra","strand","numMatches","blockLen","cg","rest","observer","next","SyntenyFeature","uniqueId","CIGAR","syntenyId","identity","mate","signal","complete","freeResources","getMismatches","MismatchParser","SimpleFeature","get","arg","parseBed","text","Map","split","f","name","score","readFile","file","buffer","TextDecoder","fatal","decode","isGzip","unzip","zip","a","b","e","i","decoder","parseLineByLine","cb","blockStart","entries","subarray","toString","trim","push","mappingQual","fields","Object","fromEntries","field","flipCigar","cigar","arr","op","swapIndelCigar","replaceAll"],"sourceRoot":""}\n\\ No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/3175.af2c93a5.chunk.js
--- a/x/static/js/3175.af2c93a5.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,2 +0,0 @@
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3175.af2c93a5.chunk.js.map
--- a/x/static/js/3175.af2c93a5.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/static/js/3199.a36b17a7.chunk.js
--- a/x/static/js/3199.a36b17a7.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3274.053c3df5.chunk.js
--- a/x/static/js/3274.053c3df5.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3274.053c3df5.chunk.js.map
--- a/x/static/js/3274.053c3df5.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3301.db457761.chunk.js.LICENSE.txt
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3304.65e5d8dd.chunk.js
--- a/x/static/js/3304.65e5d8dd.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3304.65e5d8dd.chunk.js.map
--- a/x/static/js/3304.65e5d8dd.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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n\\n}\\n\\ninterface CoreFeat {\\n stra'..b') * 10},50%,50%)`\\n }\\n } else {\\n if (type === \'orientation\' || type === \'insertSizeAndOrientation\') {\\n if (s1 === -1 && s2 === 1) {\\n ctx.strokeStyle = \'navy\'\\n } else if (s1 === 1 && s2 === -1) {\\n ctx.strokeStyle = \'green\'\\n } else {\\n ctx.strokeStyle = \'grey\'\\n }\\n } else if (type === \'gradient\') {\\n ctx.strokeStyle = `hsl(${Math.log10(absrad) * 10},50%,50%)`\\n }\\n }\\n }\\n\\n const destX = p + radius * 2\\n const destY = Math.min(height + jitter(jitterVal), absrad)\\n if (longRange) {\\n // avoid drawing gigantic circles that glitch out the rendering,\\n // instead draw vertical lines\\n if (absrad > 100_000) {\\n drawLineAtOffset(ctx, p + jitter(jitterVal), height, \'red\')\\n drawLineAtOffset(ctx, p2 + jitter(jitterVal), height, \'red\')\\n } else if (drawArcInsteadOfBezier) {\\n ctx.arc(p + radius + jitter(jitterVal), 0, absrad, 0, Math.PI)\\n ctx.stroke()\\n } else {\\n ctx.bezierCurveTo(\\n p + jitter(jitterVal),\\n destY,\\n destX,\\n destY,\\n destX + jitter(jitterVal),\\n 0,\\n )\\n ctx.stroke()\\n }\\n } else {\\n ctx.bezierCurveTo(\\n p + jitter(jitterVal),\\n destY,\\n destX,\\n destY,\\n destX + jitter(jitterVal),\\n 0,\\n )\\n ctx.stroke()\\n }\\n } else if (r1 && drawInter) {\\n drawLineAtOffset(ctx, r1 - view.offsetPx, height, \'purple\')\\n }\\n }\\n\\n for (const chain of chains) {\\n // chain.length === 1, singleton (other pairs/mates not in view)\\n if (chain.length === 1 && drawLongRange) {\\n const f = chain[0]!\\n if (hasPaired && !(f.flags & 8)) {\\n const mate = {\\n refName: f.next_ref || \'\',\\n start: f.next_pos || 0,\\n end: f.next_pos || 0,\\n strand: f.strand,\\n }\\n draw(f, mate, asm, true)\\n } else {\\n const features = [f, ...featurizeSA(f.SA, f.id, f.strand, f.name)].sort(\\n (a, b) => a.clipPos - b.clipPos,\\n )\\n for (let i = 0; i < features.length - 1; i++) {\\n const f = features[i]!\\n const v1 = features[i + 1]!\\n draw(f, v1, asm, true)\\n }\\n }\\n } else {\\n const res = hasPaired\\n ? chain.filter(f => !(f.flags & 2048) && !(f.flags & 8))\\n : chain\\n .sort((a, b) => a.clipPos - b.clipPos)\\n .filter(f => !(f.flags & 256))\\n for (let i = 0; i < res.length - 1; i++) {\\n draw(res[i]!, res[i + 1]!, asm, false)\\n }\\n }\\n }\\n}\\n","import { ChainData } from \'./fetchChains\'\\n\\nexport function hasPairedReads(features: ChainData) {\\n for (const f of features.chains.values()) {\\n if (f[0]!.flags & 1) {\\n return true\\n }\\n }\\n return false\\n}\\n"],"names":["jitter","n","Math","random","drawLineAtOffset","ctx","offset","height","color","strokeStyle","beginPath","moveTo","lineTo","stroke","drawFeats","self","width","chainData","colorBy","drawInter","drawLongRange","lineWidthSetting","jitterVal","view","getContainingView","assemblyManager","getSession","chains","stats","hasPaired","hasPairedReads","asm","get","assemblyNames","type","lineWidth","chain","length","f","flags","features","featurizeSA","SA","id","strand","name","sort","a","b","clipPos","i","draw","refName","next_ref","start","next_pos","end","res","filter","k1","k2","assembly","longRange","s1","s2","f2","p1","p2","ra1","getCanonicalRefName","ra2","r1","bpToPx","coord","offsetPx","r2","undefined","radius","absrad","abs","p","drawArcInsteadOfBezier","getPairedInsertSizeAndOrientationColor","getPairedOrientationColor","getPairedInsertSizeColor","log10","destX","destY","min","arc","PI","bezierCurveTo","values"],"sourceRoot":""}\n\\ No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/3311.92fac4a6.chunk.js
--- a/x/static/js/3311.92fac4a6.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3311.92fac4a6.chunk.js.map
--- a/x/static/js/3311.92fac4a6.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/static/js/3368.6e9b017b.chunk.js
--- a/x/static/js/3368.6e9b017b.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3384.e146a796.chunk.js
--- a/x/static/js/3384.e146a796.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3384.e146a796.chunk.js.map
--- a/x/static/js/3384.e146a796.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3416.f7c72cbe.chunk.js
--- a/x/static/js/3416.f7c72cbe.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3416.f7c72cbe.chunk.js.map
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3425.be85a6ad.chunk.js
--- a/x/static/js/3425.be85a6ad.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3474.8c1888be.chunk.js.map
--- a/x/static/js/3474.8c1888be.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3497.9db6611b.chunk.js
--- a/x/static/js/3497.9db6611b.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3497.9db6611b.chunk.js.map
--- a/x/static/js/3497.9db6611b.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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tags[tag] : feature.get(tag)\n}\n\n// use fallback alt tag, used in situations where upper case/lower case tags\n// exist e.g. Mm/MM for base modifications\nexport function getTagAlt(feature: Feature, tag: string, alt: string) {\n return getTag(feature, tag) ?? getTag(feature, alt)\n}\n\n// orientation definitions from igv.js, see also\n// https://software.broadinstitute.org/software/igv/interpreting_pair_orientations\nexport const orientationTypes = {\n fr: {\n F1R2: 'LR',\n F2R1: 'LR',\n\n F1F2: 'LL',\n F2F1: 'LL',\n\n R1R2: 'RR',\n R2R1: 'RR',\n\n R1F2: 'RL',\n R2F1: 'RL',\n } as Record<string, string>,\n\n rf: {\n R1F2: 'LR',\n R2F1: 'LR',\n\n R1R2: 'LL',\n R2R1: 'LL',\n\n F1F2: 'RR',\n F2F1: 'RR',\n\n F1R2: 'RL',\n F2R1: 'RL',\n } as Record<string, string>,\n\n ff: {\n F2F1: 'LR',\n R1R2: 'LR',\n\n F2R1: 'LL',\n R1F2: 'LL',\n\n R2F1: 'RR',\n F1R2: 'RR',\n\n R2R1: 'RL',\n F1F2: 'RL',\n } as Record<string, string>,\n}\n\nexport const pairMap = {\n LR: 'color_pair_lr',\n LL: 'color_pair_ll',\n RR: 'color_pair_rr',\n RL: 'color_pair_rl',\n} as const\n\nexport function getColorWGBS(strand: number, base: string) {\n if (strand === 1) {\n if (base === 'C') {\n return '#f00'\n }\n if (base === 'T') {\n return '#00f'\n }\n } else if (strand === -1) {\n if (base === 'G') {\n return '#f00'\n }\n if (base === 'A') {\n return '#00f'\n }\n }\n return '#888'\n}\n\n// fetches region sequence augmenting by +/- 1bp for CpG on either side of\n// requested region\nexport async function fetchSequence(\n region: AugmentedRegion,\n adapter: BaseFeatureDataAdapter,\n) {\n const { start, end, originalRefName, refName } = region\n\n const feats = await firstValueFrom(\n adapter\n .getFeatures({\n ...region,\n refName: originalRefName || refName,\n end: end + 1,\n start: Math.max(0, start - 1),\n })\n .pipe(toArray()),\n )\n return feats[0]?.get('seq')\n}\n\n// has to check underlying C-G (aka CpG) on the reference sequence\nexport function shouldFetchReferenceSequence(type?: string) {\n return type === 'methylation'\n}\n\n// adapted from IGV\n// https://github.com/igvteam/igv/blob/e803e3af2d8c9ea049961dfd4628146bdde9a574/src/main/java/org/broad/igv/sam/mods/BaseModificationColors.java#L27\nexport const modificationColors = {\n m: 'rgb(255,0,0)',\n h: 'rgb(11, 132, 165)',\n o: 'rgb(111, 78, 129)',\n f: 'rgb(246, 200, 95)',\n c: 'rgb(157, 216, 102)',\n g: 'rgb(255, 160, 86)',\n e: 'rgb(141, 221, 208)',\n b: 'rgb(202, 71, 47)',\n} as Record<string, string>\n\ntype DisplayModel = IAnyStateTreeNode & { setError: (arg: unknown) => void }\n\nexport function createAutorun(\n self: DisplayModel,\n cb: () => Promise<void>,\n opts?: IAutorunOptions,\n) {\n addDisposer(\n self,\n autorun(async () => {\n try {\n await cb()\n } catch (e) {\n if (isAlive(self)) {\n self.setError(e)\n }\n }\n }, opts),\n )\n}\nexport function randomColor() {\n return `hsl(${Math.random() * 200}, 50%, 50%)`\n}\n","import {\n dedupe,\n Feature,\n getContainingTrack,\n getContainingView,\n getSession,\n} from '@jbrowse/core/util'\nimport { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'\nimport { LinearArcDisplayModel } from './model'\n\ntype LGV = LinearGenomeViewModel\n\nexport interface ReducedFeature {\n name: string\n strand: number\n refName: string\n start: number\n end: number\n id: string\n flags: number\n tlen: number\n pair_orientation: string\n next_ref?: string\n next_pos?: number\n clipPos: number\n SA?: string\n}\n\nexport interface ChainStats {\n max: number\n min: number\n upper: number\n lower: number\n}\n\nexport interface ChainData {\n chains: ReducedFeature[][]\n stats?: ChainStats\n}\n\nexport async function fetchChains(self: LinearArcDisplayModel) {\n // @ts-expect-error\n const { rpcSessionId: sessionId } = getContainingTrack(self)\n const { rpcManager } = getSession(self)\n const view = getContainingView(self) as LGV\n\n if (!view.initialized || self.error || self.regionTooLarge) {\n return\n }\n\n self.setLoading(true)\n const ret = (await rpcManager.call(sessionId, 'CoreGetFeatures', {\n sessionId,\n regions: view.staticBlocks.contentBlocks,\n adapterConfig: self.adapterConfig,\n })) as Feature[]\n\n self.setFeatures(dedupe(ret, r => r.id()))\n self.setLoading(false)\n}\n"],"names":["doAfterAttach","self","cb","addDisposer","autorun","async","e","isAlive","setError","delay","createAutorun","rpcSessionId","sessionId","getContainingTrack","rpcManager","getSession","view","getContainingView","initialized","error","regionTooLarge","setLoading","ret","call","regions","staticBlocks","contentBlocks","adapterConfig","setFeatures","dedupe","r","id","fetchChains"],"sourceRoot":""}
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3525.e74d3ff0.chunk.js
--- a/x/static/js/3525.e74d3ff0.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3525.e74d3ff0.chunk.js.map
--- a/x/static/js/3525.e74d3ff0.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3550.089089a8.chunk.js
--- a/x/static/js/3550.089089a8.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3550.089089a8.chunk.js.map
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3578.058bdae5.chunk.js
--- a/x/static/js/3578.058bdae5.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3578.058bdae5.chunk.js.map
--- a/x/static/js/3578.058bdae5.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3614.af493134.chunk.js
--- a/x/static/js/3614.af493134.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3614.af493134.chunk.js.map
--- a/x/static/js/3614.af493134.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/366.b00bf6ca.chunk.js
--- a/x/static/js/366.b00bf6ca.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/366.b00bf6ca.chunk.js.map
--- a/x/static/js/366.b00bf6ca.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3682.840e721c.chunk.js
--- a/x/static/js/3682.840e721c.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3862.9fd8e870.chunk.js
--- a/x/static/js/3862.9fd8e870.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3862.9fd8e870.chunk.js.map
--- a/x/static/js/3862.9fd8e870.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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internal component.\\n */\\nimport { jsx as _jsx } from \\"react/jsx-runtime\\";\\nexport default createSvgIcon(/*#__PURE__*/_jsx(\\"path\\", {\\n d: \\"M20 12l-1.41-1.41L13 16.17V4h-2v12.17l-5.58-5.59L4 12l8 8 8-8z\\"\\n}), \'ArrowDownward\');","import generateUtilityClasses from \'@mui/utils/generateUtilityClasses\';\\nimport generateUtilityClass from \'@mui/utils/generateUtilityClass\';\\nexport function getTableSortLabelUtilityClass(slot) {\\n return generateUtilityClass(\'MuiTableSortLabel\', slot);\\n}\\nconst tableSortLabelClasses = generateUtilityClasses(\'MuiTableSortLabel\', [\'root\', \'active\', \'icon\', \'iconDirectionDesc\', \'iconDirectionAsc\', \'directionDesc\', \'directionAsc\']);\\nexport default tableSortLabelClasses;","\'use client\';\\n\\nimport composeClasses from \'@mui/utils/composeClasses\';\\nimport clsx from \'clsx\';\\nimport PropTypes from \'prop-types\';\\nimport * as React from \'react\';\\nimport ButtonBase from \\"../ButtonBase/index.js\\";\\nimport ArrowDownwardIcon from \\"../internal/svg-icons/ArrowDownward.js\\";\\nimport { styled } from \\"../zero-styled/index.js\\";\\nimport memoTheme from \\"../utils/memoTheme.js\\";\\nimport { useDefaultProps } from \\"../DefaultPropsProvider/index.js\\";\\nimport capitalize from \\"../utils/capitalize.js\\";\\nimport tableSortLabelClasses, { getTableSortLabelUtilityClass } from \\"./tableSortLabelClasses.js\\";\\nimport { jsx as _jsx, jsxs as _jsxs } from \\"react/jsx-runtime\\";\\nconst useUtilityClasses = ownerState => {\\n const {\\n classes,\\n direction,\\n active\\n } = ownerState;\\n const slots = {\\n root: [\'root\', active && \'active'..b' transition: theme.transitions.create([\'opacity\', \'transform\'], {\\n duration: theme.transitions.duration.shorter\\n }),\\n userSelect: \'none\',\\n variants: [{\\n props: {\\n direction: \'desc\'\\n },\\n style: {\\n transform: \'rotate(0deg)\'\\n }\\n }, {\\n props: {\\n direction: \'asc\'\\n },\\n style: {\\n transform: \'rotate(180deg)\'\\n }\\n }]\\n})));\\n\\n/**\\n * A button based label for placing inside `TableCell` for column sorting.\\n */\\nconst TableSortLabel = /*#__PURE__*/React.forwardRef(function TableSortLabel(inProps, ref) {\\n const props = useDefaultProps({\\n props: inProps,\\n name: \'MuiTableSortLabel\'\\n });\\n const {\\n active = false,\\n children,\\n className,\\n direction = \'asc\',\\n hideSortIcon = false,\\n IconComponent = ArrowDownwardIcon,\\n ...other\\n } = props;\\n const ownerState = {\\n ...props,\\n active,\\n direction,\\n hideSortIcon,\\n IconComponent\\n };\\n const classes = useUtilityClasses(ownerState);\\n return /*#__PURE__*/_jsxs(TableSortLabelRoot, {\\n className: clsx(classes.root, className),\\n component: \\"span\\",\\n disableRipple: true,\\n ownerState: ownerState,\\n ref: ref,\\n ...other,\\n children: [children, hideSortIcon && !active ? null : /*#__PURE__*/_jsx(TableSortLabelIcon, {\\n as: IconComponent,\\n className: clsx(classes.icon),\\n ownerState: ownerState\\n })]\\n });\\n});\\nprocess.env.NODE_ENV !== \\"production\\" ? 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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3902.69c7ff0c.chunk.js
--- a/x/static/js/3902.69c7ff0c.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3902.69c7ff0c.chunk.js.LICENSE.txt
--- a/x/static/js/3902.69c7ff0c.chunk.js.LICENSE.txt Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,6 +0,0 @@
-/*!
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- *
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- * @license MIT
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3902.69c7ff0c.chunk.js.map
--- a/x/static/js/3902.69c7ff0c.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3940.c8b3da50.chunk.js
--- a/x/static/js/3940.c8b3da50.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/3940.c8b3da50.chunk.js.map
--- a/x/static/js/3940.c8b3da50.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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[Badge](https://mui.com/base-ui/react-badge/#hook)\\n *\\n * API:\\n *\\n * - [useBadge API](https://mui.com/base-ui/react-badge/hooks-api/#use-badge)\\n */\\nfunction useBadge(parameters) {\\n const {\\n badgeContent: badgeContentProp,\\n invisible: invisibleProp = false,\\n max: maxProp = 99,\\n showZero = false\\n } = parameters;\\n const prevProps = usePreviousProps({\\n badgeContent: badgeContentProp,\\n max: maxProp\\n });\\n let invisible = invisibleProp;\\n if (invisibleProp === false && badgeContentProp === 0 && !showZero) {\\n invisible = true;\\n }\\n const {\\n badgeContent,\\n max = maxProp\\n } = invisible ? prevProps : parameters;\\n const displayValue = badgeContent && Number(badgeContent) > max ? `${max}+` : badgeContent;\\n return {\\n badgeContent,\\n invisible,\\n max,\\n displayValue\\n };\\n}\\nexport default useBadge;","import generateUtilityClasses from \'@mui/utils/generateUtilityClasses\';\\nimport generateUtilityClass from \'@mui/utils/generateUtilityClass\';\\nexport function getBadgeUtilityClass(slot) {\\n return generateUtilityClass(\'MuiBadge\', slot);\\n}\\nconst badgeClasses = generateUtilityClasses(\'MuiBadge\', [\'root\', \'badge\', \'dot\', \'standard\', \'anchorOriginTopRight\', \'anchorOriginBottomRight\', \'anchorOriginTopLeft\', \'anchorOriginBottomLeft\', \'invisible\', \'colorError\', \'colorInfo\', \'colorPrimary\', \'colorSecondary\', \'colorSuccess\', \'colorWarning\', \'overlapRectangular\', \'overlapCircular\',\\n// TODO: v6 remove the overlap value from these class keys\\n\'anchorOriginTopLeftCircular\', \'anchorOriginTopLeftRectangular\', \'anchorOriginTopRightCircular\', \'anchorOriginTopRightRectangular\', \'anchorOriginBottomLeftCircular\', \'anchorOriginBottomLeftRectangular\', \'anchorOriginBottomRightCircular\', \'anchorOriginBottomRightRectangular\']);\\nexport default badgeClasses;"],"names":["BadgeRoot","styled","name","slot","overridesResolver","props","styles","root","position","display","verticalAlign","flexShrink","BadgeBadge","ownerState","badge","variant","capitalize","anchorOrigin","vertical","horizontal","overlap","color","invisible","memoTheme","theme","flexDirection","flexWrap","justifyContent","alignContent","alignItems","boxSizing","fontFamily","typography","fontWeight","fontWeightMedium","fontSize","pxToRem","minWidth","RADIUS_STANDARD","lineHeight","padding","height","borderRadius","zIndex","transition","transitions","create","easing","easeInOut","duration","enteringScreen","variants","Object","entries","palette","filter","createSimplePaletteValueFilter","map","style","backgroundColor","vars","main","contrastText","RADIUS_DOT","top","right","transform","transformOrigin","badgeClasses","bottom","left","leavingScreen","inProps","ref","anchorOriginProp","className","classes","classesProp","component","components","componentsProps","children","overlapProp","colorProp","invisibleProp","max","maxProp","badgeContent","badgeContentProp","slots","slotProps","showZero","variantProp","other","invisibleFromHook","displayValue","displayValueFromHook","parameters","prevProps","usePreviousProps","Number","undefined","composeClasses","useUtilityClasses","RootSlot","Root","BadgeSlot","Badge","rootSlotProps","badgeSlotProps","rootProps","useSlotProps","elementType","externalSlotProps","externalForwardedProps","additionalProps","as","clsx","badgeProps","getBadgeUtilityClass"],"sourceRoot":""}\n\\ No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/399.e36b7683.chunk.js
--- a/x/static/js/399.e36b7683.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/399.e36b7683.chunk.js.map
--- a/x/static/js/399.e36b7683.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4033.df8ecd0d.chunk.js
--- a/x/static/js/4033.df8ecd0d.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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-"use strict";(globalThis.webpackChunk_jbrowse_web=globalThis.webpackChunk_jbrowse_web||[]).push([[4033],{34033:(e,t,a)=>{a.r(t),a.d(t,{default:()=>m});var l=a(7552),n=a(68446),r=a(49823),o=a(29499),c=a(36715),s=a(1343),i=a(58507),h=a(5401);const u=(0,a(75785).n9)()({root:{width:500}}),m=(0,n.observer)((function({model:e,handleClose:t}){const{classes:a}=u(),{maxHeight:n=""}=e,[m,d]=(0,l.useState)(`${n}`),b=""!==m&&!Number.isNaN(+m);return l.createElement(r.Dialog,{open:!0,onClose:t,title:"Set max height"},l.createElement(o.A,{className:a.root},l.createElement(c.A,null,'Set max height for the track. For example, you can increase this if the layout says "Max height reached"'),l.createElement(s.A,{value:m,onChange:e=>{d(e.target.value)},placeholder:"Enter max score"}),b?null:l.createElement("div",{style:{color:"red"}},"Invalid number")),l.createElement(i.A,null,l.createElement(h.A,{variant:"contained",color:"primary",type:"submit",autoFocus:!0,disabled:!b,onClick:()=>{e.setMaxHeight(+m),t()}},"Submit"),l.createElement(h.A,{variant:"contained",color:"secondary",onClick:()=>{t()}},"Cancel")))}))}}]);
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4033.df8ecd0d.chunk.js.map
--- a/x/static/js/4033.df8ecd0d.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4060.8757dbe8.chunk.js
--- a/x/static/js/4060.8757dbe8.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4060.8757dbe8.chunk.js.map
--- a/x/static/js/4060.8757dbe8.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4133.451f5e47.chunk.js
--- a/x/static/js/4133.451f5e47.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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-"use strict";(globalThis.webpackChunk_jbrowse_web=globalThis.webpackChunk_jbrowse_web||[]).push([[4138],{44138:(e,n,o)=>{o.r(n),o.d(n,{default:()=>d});var t=o(7552),c=o(33371),a=o(32808),r=o(36715),s=o(29499),i=o(58507),l=o(5401),m=o(49823),b=o(75785),u=o(68446),C=o(68584);const f=(0,b.n9)()((e=>({connectionContainer:{width:500,margin:e.spacing(4)}}))),h=(0,u.observer)((function({conf:e,session:n,breakConnection:o}){const{connectionInstances:r=[]}=n,s=(0,C.readConfObject)(e,"name"),i=(0,C.readConfObject)(e,"assemblyNames"),l=r.find((e=>s===e.name));return t.createElement(c.A,{key:e.connectionId,control:t.createElement(a.A,{checked:!!l,onChange:()=>{l?o(e):n.makeConnection?.(e)},color:"primary"}),label:[s,i.length?`(${m=i.join(","),m.length>20?`${m.slice(0,20)}...`:m})`:""].filter((e=>!!e)).join(" ")});var m})),k=(0,u.observer)((function({session:e,breakConnection:n}){const{classes:o}=f();return t.createElement("div",{className:o.connectionContainer},e.connections.length?e.connections.map(((o,c)=>t.createElement("div",{key:`${o.name}_${c}`},t.createElement(h,{conf:o,session:e,breakConnection:n})))):t.createElement(r.A,null,"No connections found"))})),d=(0,u.observer)((function({session:e,handleClose:n,breakConnection:o}){return t.createElement(m.Dialog,{open:!0,onClose:n,maxWidth:"lg",title:"Turn on/off connections"},t.createElement(s.A,null,t.createElement(r.A,null,"Use the checkbox to turn on/off connections"),t.createElement(k,{session:e,breakConnection:o})),t.createElement(i.A,null,t.createElement(l.A,{onClick:()=>{n()},variant:"contained",color:"primary"},"Close")))}))}}]);
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4138.57ad92a3.chunk.js.map
--- a/x/static/js/4138.57ad92a3.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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[

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\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/static/js/419.021427b6.chunk.js
--- a/x/static/js/419.021427b6.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/419.021427b6.chunk.js.map
--- a/x/static/js/419.021427b6.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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could possibly be moved into a higher directory and shared between the two\\nimport { toUrlSafeB64 } from \'./utils\'\\n\\n// from https://stackoverflow.com/questions/1349404/\\nfunction generateUID(length: number) {\\n return window\\n .btoa(\\n [...window.crypto.getRandomValues(new Uint8Array(length * 2))]\\n .map(b => String.fromCharCode(b))\\n .join(\'\'),\\n )\\n .replaceAll(/[+/]/g, \'\')\\n .slice(0, length)\\n}\\n\\nconst encrypt = async (text: string, password: string) => {\\n const AES = await import(\'crypto-js/aes\')\\n return AES.encrypt(text, password).toString()\\n}\\n\\nconst decrypt = async (text: string, password: string) => {\\n const AES = await import(\'crypto-js/aes\')\\n const Utf8 = await import(\'crypto-js/enc-utf8\')\\n const bytes = AES.decrypt(text, password)\\n return bytes.toString(Utf8)\\n}\\n\\nfunction getErrorMsg(err: string) {\\n try {\\n const obj = JSON.parse(err)\\n return obj.message\\n } catch (e) {\\n return err\\n }\\n}\\n// writes the encrypted session, current datetime, and referer to DynamoDB\\nexport async function shareSessionToDynamo(\\n session: unknown,\\n url: string,\\n referer: string,\\n) {\\n const sess = await toUrlSafeB64(JSON.stringify(session))\\n const password = generateUID(5)\\n const encryptedSession = await encrypt(sess, password)\\n\\n const data = new FormData()\\n data.append(\'session\', encryptedSession)\\n data.append(\'dateShared\', `${Date.now()}`)\\n data.append(\'referer\', referer)\\n\\n const response = await fetch(`${url}share`, {\\n method: \'POST\',\\n mode: \'cors\',\\n body: data,\\n })\\n\\n if (!response.ok) {\\n const err = await response.text()\\n throw new Error(getErrorMsg(err))\\n }\\n const json = await response.json()\\n return {\\n json,\\n encryptedSession,\\n password,\\n }\\n}\\n\\nexport async function readSessionFromDynamo(\\n baseUrl: string,\\n sessionQueryParam: string,\\n password: string,\\n signal?: AbortSignal,\\n) {\\n const sessionId = sessionQueryParam.split(\'share-\')[1]!\\n const url = `${baseUrl}?sessionId=${encodeURIComponent(sessionId)}`\\n const response = await fetch(url, {\\n signal,\\n })\\n\\n if (!response.ok) {\\n const err = await response.text()\\n throw new Error(getErrorMsg(err))\\n }\\n\\n const json = await response.json()\\n return decrypt(json.session, password)\\n}\\n"],"names":["useStyles","makeStyles","flexItem","margin","content","display","flexFlow","gap","observer","onClose","model","classes","url","setUrl","useState","error","setError","loading","setLoading","session","getSession","selectedBookmarks","shareAll","length","bookmarksToShare","allBookmarksModel","sharedBookmarksModel","useEffect","isSessionWithShareURL","Error","snap","getSnapshot","locationUrl","URL","window","location","href","result","shareSessionToDynamo","shareURL","params","URLSearchParams","search","set","json","sessionId","password","toString","e","React","Dialog","open","title","DialogContent","className","Alert","severity","DialogContentText","ErrorMessage","Typography","TextField","label","value","slotProps","input","readOnly","variant","fullWidth","onClick","event","target","select","DialogActions","Button","color","disabled","startIcon","ContentCopyIcon","async","copy","notify","encrypt","text","decrypt","AES","Utf8","getErrorMsg","err","JSON","parse","message","referer","sess","toUrlSafeB64","stringify","btoa","crypto","getRandomValues","Uint8Array","map","b","String","fromCharCode","join","replaceAll","slice","encryptedSession","data","FormData","append","Date","now","response","fetch","method","mode","body","ok","readSessionFromDynamo","baseUrl","sessionQueryParam","signal","split","encodeURIComponent"],"sourceRoot":""}\n\\ No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/4234.63e1ba57.chunk.js
--- a/x/static/js/4234.63e1ba57.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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-"use strict";(globalThis.webpackChunk_jbrowse_web=globalThis.webpackChunk_jbrowse_web||[]).push([[4234],{14234:(e,t,a)=>{a.r(t),a.d(t,{default:()=>c});var s=a(93902),r=a(46377),i=a(99834),n=a(99546),u=a(66885),o=a(37957);class c extends r.BaseFeatureDataAdapter{static capabilities=["hasResolution","hasLocalStats","hasGlobalStats"];async setupPre(e){const{statusCallback:t=()=>{}}=e||{},a=this.pluginManager,r=new s.j({filehandle:(0,i.openLocation)(this.getConf("bigWigLocation"),a)}),u=await(0,n.updateStatus)("Downloading bigwig header",t,(()=>r.getHeader(e)));return{bigwig:r,header:u}}async setup(e){return this.setupP||(this.setupP=this.setupPre(e).catch((e=>{throw this.setupP=void 0,e}))),this.setupP}async getRefNames(e){const{header:t}=await this.setup(e);return Object.keys(t.refsByName)}async refIdToName(e){const{header:t}=await this.setup();return t.refsByNumber[e]?.name}async getGlobalStats(e){const{header:t}=await this.setup(e);return(0,o.WD)(t.totalSummary)}getFeatures(e,t={}){const{refName:a,start:s,end:r}=e,{bpPerPx:i=0,signal:n,resolution:o=1,statusCallback:c=()=>{}}=t;return(0,u.ObservableCreate)((async n=>{c("Downloading bigwig data");const u=this.getConf("source"),{bigwig:h}=await this.setup(t),l=await h.getFeatures(a,s,r,{...t,basesPerSpan:i/o});for(const t of l){u&&(t.source=u);const s=`${u}:${e.refName}:${t.start}-${t.end}`;t.refName=a,t.uniqueId=s,n.next({get:e=>t[e],id:()=>s,toJSON:()=>t})}n.complete()}),n)}async getMultiRegionFeatureDensityStats(e){return{featureDensity:0}}freeResources(){}}}}]);
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4234.63e1ba57.chunk.js.map
--- a/x/static/js/4234.63e1ba57.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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{ BigWig } from '@gmod/bbi'\nimport {\n BaseFeatureDataAdapter,\n BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { AugmentedRegion as Region } from '@jbrowse/core/util/types'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { updateStatus, Feature } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport {\n rectifyStats,\n UnrectifiedQuantitativeStats,\n} from '@jbrowse/core/util/stats'\n\ninterface WiggleOptions extends BaseOptions {\n resolution?: number\n}\n\nexport default class BigWigAdapter extends BaseFeatureDataAdapter {\n private setupP?: Promise<{\n bigwig: BigWig\n header: Awaited<ReturnType<BigWig['getHeader']>>\n }>\n\n public static capabilities = [\n 'hasResolution',\n 'hasLocalStats',\n 'hasGlobalStats',\n ]\n\n private async setupPre(opts?: BaseOptions) {\n const { statusCallback = () => {} } = opts || {}\n const pm = this.pluginManager\n const bigwig = new BigWig({\n filehandle: openLocation(this.getConf('bigWigLocation'), pm),\n })\n const header = await updateStatus(\n 'Downloading bigwig header',\n statusCallback,\n () => bigwig.getHeader(opts),\n )\n return { bigwig, header }\n }\n\n async setup(opts?: BaseOptions) {\n if (!this.setupP) {\n this.setupP = this.setupPre(opts).catch((e: unknown) => {\n this.setupP = undefined\n throw e\n })\n }\n return this.setupP\n }\n\n public async getRefNames(opts?: BaseOptions) {\n const { header } = await this.setup(opts)\n return Object.keys(header.refsByName)\n }\n\n public async refIdToName(refId: number) {\n const { header } = await this.setup()\n return header.refsByNumber[refId]?.name\n }\n\n public async getGlobalStats(opts?: BaseOptions) {\n const { header } = await this.setup(opts)\n return rectifyStats(header.totalSummary as UnrectifiedQuantitativeStats)\n }\n\n public getFeatures(region: Region, opts: WiggleOptions = {}) {\n const { refName, start, end } = region\n const {\n bpPerPx = 0,\n signal,\n resolution = 1,\n statusCallback = () => {},\n } = opts\n return ObservableCreate<Feature>(async observer => {\n statusCallback('Downloading bigwig data')\n const source = this.getConf('source')\n const { bigwig } = await this.setup(opts)\n const feats = await bigwig.getFeatures(refName, start, end, {\n ...opts,\n basesPerSpan: bpPerPx / resolution,\n })\n\n for (const data of feats) {\n if (source) {\n // @ts-expect-error\n data.source = source\n }\n const uniqueId = `${source}:${region.refName}:${data.start}-${data.end}`\n // @ts-expect-error\n data.refName = refName\n data.uniqueId = uniqueId\n observer.next({\n // @ts-expect-error\n get: (str: string) => (data as Record<string, unknown>)[str],\n id: () => uniqueId,\n // @ts-expect-error\n toJSON: () => data,\n })\n }\n observer.complete()\n }, signal)\n }\n\n // always render bigwig instead of calculating a feature density for it\n async getMultiRegionFeatureDensityStats(_regions: Region[]) {\n return { featureDensity: 0 }\n }\n\n public freeResources(): void {}\n}\n"],"names":["BigWigAdapter","BaseFeatureDataAdapter","setupPre","opts","statusCallback","pm","this","pluginManager","bigwig","BigWig","filehandle","openLocation","getConf","header","updateStatus","getHeader","setup","setupP","catch","e","undefined","getRefNames","Object","keys","refsByName","refIdToName","refId","refsByNumber","name","getGlobalStats","rectifyStats","totalSummary","getFeatures","region","refName","start","end","bpPerPx","signal","resolution","ObservableCreate","async","source","feats","basesPerSpan","data","uniqueId","observer","next","get","str","id","toJSON","complete","getMultiRegionFeatureDensityStats","_regions","featureDensity","freeResources"],"sourceRoot":""}
\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/static/js/4284.61dbc58f.chunk.js
--- a/x/static/js/4284.61dbc58f.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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-"use strict";(globalThis.webpackChunk_jbrowse_web=globalThis.webpackChunk_jbrowse_web||[]).push([[4284,7706],{94284:(e,t,n)=>{n.r(t),n.d(t,{default:()=>o});var r=n(7706),i=n(99546),a=n(99834),s=n(46377);class o extends s.BaseAdapter{async getData(){const e=this.pluginManager,t=this.getConf("cytobandLocation");if(""===t.uri||"/path/to/cytoband.txt.gz"===t.uri)return[];const n=await(0,a.openLocation)(t,e).readFile(),s=(0,i.isGzip)(n)?await(0,r.unzip)(n):n;return new TextDecoder("utf8",{fatal:!0}).decode(s).split(/\n|\r\n|\r/).filter((e=>!!e.trim())).map(((e,t)=>{const[n,r,a,s,o]=e.split("\t");return new i.SimpleFeature({uniqueId:`${t}`,refName:n,start:+r,end:+a,name:s,type:o})}))}freeResources(){}}},7706:(e,t,n)=>{n.d(t,{sG:()=>d,unzip:()=>s,i2:()=>o});var r=n(35451),i=n(45834),a=n(57864);async function s(e){try{let t,n=0,i=0;const s=[];let o,l=0;do{const r=e.subarray(n);if(o=new a.Inflate,({strm:t}=o),o.push(r,a.Z_SYNC_FLUSH),o.err)throw new Error(o.msg);n+=t.next_in,s[i]=o.result,l+=s[i].length,i+=1}while(t.avail_in);const h=new Uint8Array(l);for(let e=0,t=0;e<s.length;e++)h.set(s[e],t),t+=s[e].length;return r.hp.from(h)}catch(e){if(`${e}`.match(/incorrect header check/))throw new Error("problem decompressing block: incorrect gzip header check");throw e}}async function o(e,t){try{let n;const{minv:i,maxv:s}=t;let o=i.blockPosition,l=i.dataPosition;const h=[],c=[],d=[];let f=0,w=0;do{const t=e.subarray(o-i.blockPosition),r=new a.Inflate;if(({strm:n}=r),r.push(t,a.Z_SYNC_FLUSH),r.err)throw new Error(r.msg);const u=r.result;h.push(u);let g=u.length;c.push(o),d.push(l),1===h.length&&i.dataPosition&&(h[0]=h[0].subarray(i.dataPosition),g=h[0].length);const p=o;if(o+=n.next_in,l+=g,p>=s.blockPosition){h[w]=h[w].subarray(0,s.blockPosition===i.blockPosition?s.dataPosition-i.dataPosition+1:s.dataPosition+1),c.push(o),d.push(l),f+=h[w].length;break}f+=h[w].length,w++}while(n.avail_in);const u=new Uint8Array(f);for(let e=0,t=0;e<h.length;e++)u.set(h[e],t),t+=h[e].length;return{buffer:r.hp.from(u),cpositions:c,dpositions:d}}catch(e){if(`${e}`.match(/incorrect header check/))throw new Error("problem decompressing block: incorrect gzip header check");throw e}}var l=n(59086),h=n.n(l);class c{constructor({filehandle:e,path:t}){if(e)this.filehandle=e;else{if(!t)throw new TypeError("either filehandle or path must be defined");this.filehandle=new i.EY(t)}}_readLongWithOverflow(e,t=0,n=!0){const r=h().fromBytesLE(e.slice(t,t+8),n);if(r.greaterThan(Number.MAX_SAFE_INTEGER)||r.lessThan(Number.MIN_SAFE_INTEGER))throw new TypeError("integer overflow");return r.toNumber()}_getIndex(){return this.index||(this.index=this._readIndex()),this.index}async _readIndex(){let e=r.hp.allocUnsafe(8);await this.filehandle.read(e,0,8,0);const t=this._readLongWithOverflow(e,0,!0);if(!t)return[[0,0]];const n=new Array(t+1);n[0]=[0,0];const i=16*t;if(i>Number.MAX_SAFE_INTEGER)throw new TypeError("integer overflow");e=r.hp.allocUnsafe(i),await this.filehandle.read(e,0,i,8);for(let r=0;r<t;r+=1){const t=this._readLongWithOverflow(e,16*r),i=this._readLongWithOverflow(e,16*r+8);n[r+1]=[t,i]}return n}async getLastBlock(){const e=await this._getIndex();if(e.length)return e[e.length-1]}async getRelevantBlocksForRead(e,t){const n=t+e;if(0===e)return[];const r=await this._getIndex(),i=[],a=(e,n)=>{const r=e[1],i=n?n[1]:1/0;return r<=t&&i>t?0:r<t?-1:1};let s=0,o=r.length-1,l=Math.floor(r.length/2),h=a(r[l],r[l+1]);for(;0!==h;)h>0?o=l-1:h<0&&(s=l+1),l=Math.ceil((o-s)/2)+s,h=a(r[l],r[l+1]);i.push(r[l]);let c=l+1;for(;c<r.length&&(i.push(r[c]),!(r[c][1]>=n));c+=1);return i[i.length-1][1]<n&&i.push([]),i}}class d{constructor({filehandle:e,path:t,gziFilehandle:n,gziPath:r}){if(e)this.filehandle=e;else{if(!t)throw new TypeError("either filehandle or path must be defined");this.filehandle=new i.EY(t)}if(!n&&!r&&!t)throw new TypeError("either gziFilehandle or gziPath must be defined");this.gzi=new c({filehandle:n,path:n||r||!t?`${t}.gzi`:r})}async stat(){const e=await this.filehandle.stat();return Object.assign(e,{size:await this.getUncompressedFileSize(),blocks:void 0,blksize:void 0})}async getUncompressedFileSize(){const[,e]=await this.gzi.getLastBlock(),{size:t}=await this.filehandle.stat(),n=r.hp.allocUnsafe(4),{bytesRead:i}=await this.filehandle.read(n,0,4,t-28-4);if(4!==i)throw new Error("read error");return e+n.readUInt32LE(0)}async _readAndUncompressBlock(e,[t],[n]){let r=n;r||(r=(await this.filehandle.stat()).size);const i=r-t;return await this.filehandle.read(e,0,i,t),await s(e.slice(0,i))}async read(e,t,n,i){const a=await this.gzi.getRelevantBlocksForRead(n,i),s=r.hp.allocUnsafe(65536);let o=t,l=0;for(let t=0;t<a.length-1;t+=1){const r=await this._readAndUncompressBlock(s,a[t],a[t+1]),[,h]=a[t],c=h>=i?0:i-h,d=Math.min(i+n,h+r.length)-h;c>=0&&c<r.length&&(r.copy(e,o,c,d),o+=d-c,l+=d-c)}return{bytesRead:l,buffer:e}}}}}]);
-//# sourceMappingURL=4284.61dbc58f.chunk.js.map
\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/static/js/4284.61dbc58f.chunk.js.map
--- a/x/static/js/4284.61dbc58f.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4345.0a9072cc.chunk.js
--- a/x/static/js/4345.0a9072cc.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4345.0a9072cc.chunk.js.map
--- a/x/static/js/4345.0a9072cc.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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aligned** as that allows\\n * you to add them up quickly in your head without having to worry about decimals.\\n * @default \'inherit\'\\n */\\n align: PropTypes.oneOf([\'center\', \'inherit\', \'justify\', \'left\', \'right\']),\\n /**\\n * The content of the component.\\n */\\n children: PropTypes.node,\\n /**\\n * Override or extend the styles applied to the component.\\n */\\n classes: PropTypes.object,\\n /**\\n * @ignore\\n */\\n className: PropTypes.string,\\n /**\\n * The component used for the root node.\\n * Either a string to use a HTML element or a component.\\n */\\n component: PropTypes.elementType,\\n /**\\n * Sets the padding applied to the cell.\\n * The prop defaults to the value (`\'default\'`) inherited from the parent Table component.\\n */\\n padding: PropTypes.oneOf([\'checkbox\', \'none\', \'normal\']),\\n /**\\n * Set scope attribute.\\n */\\n scope: PropTypes.string,\\n /**\\n * Specify the size of the cell.\\n * The prop defaults to the value (`\'medium\'`) inherited from the parent Table component.\\n */\\n size: PropTypes /* @typescript-to-proptypes-ignore */.oneOfType([PropTypes.oneOf([\'medium\', \'small\']), PropTypes.string]),\\n /**\\n * Set aria-sort direction.\\n */\\n sortDirection: PropTypes.oneOf([\'asc\', \'desc\', false]),\\n /**\\n * The system prop that allows defining system overrides as well as additional CSS styles.\\n */\\n sx: PropTypes.oneOfType([PropTypes.arrayOf(PropTypes.oneOfType([PropTypes.func, PropTypes.object, PropTypes.bool])), PropTypes.func, PropTypes.object]),\\n /**\\n * Specify the cell type.\\n * The prop defaults to the value inherited from the parent TableHead, TableBody, or TableFooter components.\\n */\\n variant: PropTypes /* @typescript-to-proptypes-ignore */.oneOfType([PropTypes.oneOf([\'body\', \'footer\', \'head\']), PropTypes.string])\\n} : void 0;\\nexport default TableCell;","import generateUtilityClasses from \'@mui/utils/generateUtilityClasses\';\\nimport generateUtilityClass from \'@mui/utils/generateUtilityClass\';\\nexport function getTableCellUtilityClass(slot) {\\n return generateUtilityClass(\'MuiTableCell\', slot);\\n}\\nconst tableCellClasses = generateUtilityClasses(\'MuiTableCell\', [\'root\', \'head\', \'body\', \'footer\', \'sizeSmall\', \'sizeMedium\', \'paddingCheckbox\', \'paddingNone\', \'alignLeft\', \'alignCenter\', \'alignRight\', \'alignJustify\', \'stickyHeader\']);\\nexport default tableCellClasses;"],"names":["TableCellRoot","name","slot","overridesResolver","props","styles","ownerState","root","variant","size","padding","align","stickyHeader","theme","typography","body2","display","verticalAlign","borderBottom","vars","palette","TableCell","border","mode","divider","textAlign","variants","style","color","text","primary","lineHeight","pxToRem","fontWeight","fontWeightMedium","secondary","fontSize","paddingCheckbox","width","flexDirection","position","top","zIndex","backgroundColor","background","default","inProps","ref","className","component","componentProp","paddingProp","scope","scopeProp","sizeProp","sortDirection","variantProp","other","table","tablelvl2","isHeadCell","undefined","classes","slots","useUtilityClasses","ariaSort","as","getTableCellUtilityClass"],"sourceRoot":""}\n\\ No newline at end of file\n'

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--- a/x/static/js/4456.93a06b74.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4456.93a06b74.chunk.js.map
--- a/x/static/js/4456.93a06b74.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4499.3f0b2e70.chunk.js
--- a/x/static/js/4499.3f0b2e70.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,2 +0,0 @@\n-"use strict";(globalThis.webpackChunk_jbrowse_web=globalThis.webpackChunk_jbrowse_web||[]).push([[4499,7706],{7706:(t,e,r)=>{r.d(e,{sG:()=>u,unzip:()=>o,i2:()=>s});var i=r(35451),l=r(45834),n=r(57864);async function o(t){try{let e,r=0,l=0;const o=[];let s,h=0;do{const i=t.subarray(r);if(s=new n.Inflate,({strm:e}=s),s.push(i,n.Z_SYNC_FLUSH),s.err)throw new Error(s.msg);r+=e.next_in,o[l]=s.result,h+=o[l].length,l+=1}while(e.avail_in);const a=new Uint8Array(h);for(let t=0,e=0;t<o.length;t++)a.set(o[t],e),e+=o[t].length;return i.hp.from(a)}catch(t){if(`${t}`.match(/incorrect header check/))throw new Error("problem decompressing block: incorrect gzip header check");throw t}}async function s(t,e){try{let r;const{minv:l,maxv:o}=e;let s=l.blockPosition,h=l.dataPosition;const a=[],c=[],u=[];let _=0,p=0;do{const e=t.subarray(s-l.blockPosition),i=new n.Inflate;if(({strm:r}=i),i.push(e,n.Z_SYNC_FLUSH),i.err)throw new Error(i.msg);const m=i.result;a.push(m);let 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c=h+1;for(;c<i.length&&(l.push(i[c]),!(i[c][1]>=r));c+=1);return l[l.length-1][1]<r&&l.push([]),l}}class u{constructor({filehandle:t,path:e,gziFilehandle:r,gziPath:i}){if(t)this.filehandle=t;else{if(!e)throw new TypeError("either filehandle or path must be defined");this.filehandle=new l.EY(e)}if(!r&&!i&&!e)throw new TypeError("either gziFilehandle or gziPath must be defined");this.gzi=new c({filehandle:r,path:r||i||!e?`${e}.gzi`:i})}async stat(){const t=await this.filehandle.stat();return Object.assign(t,{size:await this.getUncompressedFileSize(),blocks:void 0,blksize:void 0})}async getUncompressedFileSize(){const[,t]=await this.gzi.getLastBlock(),{size:e}=await this.filehandle.stat(),r=i.hp.allocUnsafe(4),{bytesRead:l}=await this.filehandle.read(r,0,4,e-28-4);if(4!==l)throw new Error("read error");return t+r.readUInt32LE(0)}async _readAndUncompressBlock(t,[e],[r]){let i=r;i||(i=(await this.filehandle.stat()).size);const l=i-e;return await this.filehandle.read(t,0,l,e),await 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r,i=t;for(;i&&i!==this.nil_node;)i.less_than(e)?i.intersect(e)?(r=i,i=i.left):i=i.right:(r&&!i.less_than(r)||(r=i),i=i.left);return r||null}tree_search_interval(t,e,r){null!=t&&t!==this.nil_node&&(t.left===this.nil_node||t.not_intersect_left_subtree(e)||this.tree_search_interval(t.left,e,r),t.intersect(e)&&r.push(t),t.right===this.nil_node||t.not_intersect_right_subtree(e)||this.tree_search_interval(t.right,e,r))}tree_find_any_interval(t,e){let r=!1;return null!=t&&t!==this.nil_node&&(t.left===this.nil_node||t.not_intersect_left_subtree(e)||(r=this.tree_find_any_interval(t.left,e)),r||(r=t.intersect(e)),r||t.right===this.nil_node||t.not_intersect_right_subtree(e)||(r=this.tree_find_any_interval(t.right,e))),r}local_minimum(t){let e=t;for(;null!=e.left&&e.left!==this.nil_node;)e=e.left;return e}local_maximum(t){let e=t;for(;null!=e.right&&e.right!==this.nil_node;)e=e.right;return e}tree_successor(t){let e,r,i;if(t.right!==this.nil_node)e=this.local_minimum(t.right);else{for(r=t,i=t.parent;null!=i&&i.right===r;)r=i,i=i.parent;e=i}return e}rotate_left(t){let e=t.right;t.right=e.left,e.left!==this.nil_node&&(e.left.parent=t),e.parent=t.parent,t===this.root?this.root=e:t===t.parent.left?t.parent.left=e:t.parent.right=e,e.left=t,t.parent=e,null!=t&&t!==this.nil_node&&t.update_max(),e=t.parent,null!=e&&e!==this.nil_node&&e.update_max()}rotate_right(t){let e=t.left;t.left=e.right,e.right!==this.nil_node&&(e.right.parent=t),e.parent=t.parent,t===this.root?this.root=e:t===t.parent.left?t.parent.left=e:t.parent.right=e,e.right=t,t.parent=e,null!==t&&t!==this.nil_node&&t.update_max(),e=t.parent,null!=e&&e!==this.nil_node&&e.update_max()}tree_walk(t,e){null!=t&&t!==this.nil_node&&(this.tree_walk(t.left,e),e(t),this.tree_walk(t.right,e))}testRedBlackProperty(){let t=!0;return this.tree_walk(this.root,(function(e){0===e.color&&(1===e.left.color&&1===e.right.color||(t=!1))})),t}testBlackHeightProperty(t){let e=0,r=0,i=0;if(1===t.color&&e++,r=t.left!==this.nil_node?this.testBlackHeightProperty(t.left):1,i=t.right!==this.nil_node?this.testBlackHeightProperty(t.right):1,r!==i)throw new Error("Red-black height property violated");return e+=r,e}}}}]);\n-//# sourceMappingURL=4499.3f0b2e70.chunk.js.map\n\\ No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/4499.3f0b2e70.chunk.js.map
--- a/x/static/js/4499.3f0b2e70.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/457.6d7b716d.chunk.js
--- a/x/static/js/457.6d7b716d.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/457.6d7b716d.chunk.js.map
--- a/x/static/js/457.6d7b716d.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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onChange={event => {\\n setCopyTracks(event.target.checked)\\n }}\\n />\\n\\n <TextField\\n label=\\"Window size (bp)\\"\\n value={windowSize}\\n onChange={event => {\\n setWindowSize(event.target.value)\\n }}\\n />\\n </DialogContent>\\n <DialogActions>\\n <Button\\n onClick={() => {\\n const session = getSession(model)\\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\\n ;(async () => {\\n try {\\n const assembly = session.assemblyManager.get(assemblyName)\\n const w = +windowSize\\n if (Number.isNaN(w)) {\\n throw new Error(\'windowSize not a number\')\\n }\\n const { refName, pos, mateRefName, matePos } =\\n // @ts-expect-error\\n viewType.getBreakendCoveringRegions({ feature, assembly })\\n\\n const breakpointSplitView = session.addView(\\n \'BreakpointSplitView\',\\n {\\n type: \'BreakpointSplitView\',\\n displayName: `${\\n feature.get(\'name\') || feature.get(\'id\') || \'breakend\'\\n } split detail`,\\n views: [\\n {\\n type: \'LinearGenomeView\',\\n tracks: stripIds(getSnapshot(view.tracks)),\\n },\\n ],\\n },\\n ) as unknown as { views: LinearGenomeViewModel[] }\\n\\n await breakpointSplitView.views[0]!.navToLocations(\\n gatherOverlaps(\\n [\\n {\\n refName,\\n start: Math.max(0, pos - w),\\n end: pos + w,\\n assemblyName,\\n },\\n {\\n refName: mateRefName,\\n start: Math.max(0, matePos - w),\\n end: matePos + w,\\n assemblyName,\\n },\\n ],\\n w,\\n ),\\n )\\n } catch (e) {\\n console.error(e)\\n session.notify(`${e}`)\\n }\\n })()\\n handleClose()\\n }}\\n variant=\\"contained\\"\\n color=\\"primary\\"\\n autoFocus\\n >\\n OK\\n </Button>\\n <Button\\n color=\\"secondary\\"\\n variant=\\"contained\\"\\n onClick={() => {\\n handleClose()\\n }}\\n >\\n Cancel\\n </Button>\\n </DialogActions>\\n </Dialog>\\n )\\n})\\n\\nexport default 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No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/4615.dc35870f.chunk.js
--- a/x/static/js/4615.dc35870f.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4629.1f1a55a3.chunk.js
--- a/x/static/js/4629.1f1a55a3.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4629.1f1a55a3.chunk.js.map
--- a/x/static/js/4629.1f1a55a3.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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Link.propTypes /* remove-proptypes */ = {\\n // \xe2\x94\x8c\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80 Warning \xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x90\\n // \xe2\x94\x82 These PropTypes are generated from the TypeScript type definitions. \xe2\x94\x82\\n // \xe2\x94\x82 To update them, edit the d.ts file and run `pnpm proptypes`. \xe2\x94\x82\\n // \xe2\x94\x94\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x98\\n /**\\n * The content of the component.\\n */\\n children: PropTypes.node,\\n /**\\n * Override or extend the styles applied to the component.\\n */\\n classes: PropTypes.object,\\n /**\\n * @ignore\\n */\\n className: PropTypes.string,\\n /**\\n * The color of the link.\\n * @default \'primary\'\\n */\\n color: PropTypes /* @typescript-to-proptypes-ignore */.oneOfType([PropTypes.oneOf([\'primary\', \'secondary\', \'success\', \'error\', \'info\', \'warning\', \'textPrimary\', \'textSecondary\', \'textDisabled\']), PropTypes.string]),\\n /**\\n * The component used for the root node.\\n * Either a string to use a HTML element or a component.\\n */\\n component: elementTypeAcceptingRef,\\n /**\\n * @ignore\\n */\\n onBlur: PropTypes.func,\\n /**\\n * @ignore\\n */\\n onFocus: PropTypes.func,\\n /**\\n * @ignore\\n */\\n style: PropTypes.object,\\n /**\\n * The system prop that allows defining system overrides as well as additional CSS styles.\\n */\\n sx: PropTypes.oneOfType([PropTypes.arrayOf(PropTypes.oneOfType([PropTypes.func, PropTypes.object, PropTypes.bool])), PropTypes.func, PropTypes.object]),\\n /**\\n * `classes` prop applied to the [`Typography`](https://mui.com/material-ui/api/typography/) element.\\n */\\n TypographyClasses: PropTypes.object,\\n /**\\n * Controls when the link should have an underline.\\n * @default \'always\'\\n */\\n underline: PropTypes.oneOf([\'always\', \'hover\', \'none\']),\\n /**\\n * Applies the theme typography styles.\\n * @default \'inherit\'\\n */\\n variant: PropTypes /* @typescript-to-proptypes-ignore */.oneOfType([PropTypes.oneOf([\'body1\', \'body2\', \'button\', \'caption\', \'h1\', \'h2\', \'h3\', \'h4\', \'h5\', \'h6\', \'inherit\', \'overline\', \'subtitle1\', \'subtitle2\']), PropTypes.string])\\n} : void 0;\\nexport default Link;","import generateUtilityClasses from \'@mui/utils/generateUtilityClasses\';\\nimport generateUtilityClass from \'@mui/utils/generateUtilityClass\';\\nexport function getLinkUtilityClass(slot) {\\n return generateUtilityClass(\'MuiLink\', slot);\\n}\\nconst linkClasses = generateUtilityClasses(\'MuiLink\', [\'root\', \'underlineNone\', \'underlineHover\', \'underlineAlways\', \'button\', \'focusVisible\']);\\nexport default linkClasses;"],"names":["theme","ownerState","transformedColor","color","channelColor","v6Colors","primary","secondary","error","info","success","warning","textPrimary","textSecondary","textDisabled","LinkRoot","styled","Typography","name","slot","overridesResolver","props","styles","root","capitalize","underline","component","button","memoTheme","variants","style","textDecoration","textDecorationColor","Object","entries","palette","filter","createSimplePaletteValueFilter","map","vars","mainChannel","main","text","primaryChannel","secondaryChannel","disabled","position","WebkitTapHighlightColor","backgroundColor","outline","border","margin","borderRadius","padding","cursor","userSelect","verticalAlign","MozAppearance","WebkitAppearance","borderStyle","linkClasses","focusVisible","inProps","ref","useTheme","className","onBlur","onFocus","TypographyClasses","variant","sx","other","setFocusVisible","classes","slots","composeClasses","useUtilityClasses","clsx","event","isFocusVisible","target","undefined","Array","isArray","getLinkUtilityClass"],"sourceRoot":""}\n\\ No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/4630.f0bdb9f0.chunk.js
--- a/x/static/js/4630.f0bdb9f0.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4630.f0bdb9f0.chunk.js.map
--- a/x/static/js/4630.f0bdb9f0.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4659.b65d8547.chunk.js
--- a/x/static/js/4659.b65d8547.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4704.9b3995ff.chunk.js
--- a/x/static/js/4704.9b3995ff.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4704.9b3995ff.chunk.js.map
--- a/x/static/js/4704.9b3995ff.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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onChange={event => {\\n setCopyTracks(event.target.checked)\\n }}\\n />\\n\\n <TextField\\n label=\\"Window size (bp)\\"\\n value={windowSize}\\n onChange={event => {\\n setWindowSize(event.target.value)\\n }}\\n />\\n </DialogContent>\\n <DialogActions>\\n <Button\\n onClick={() => {\\n const session = getSession(model)\\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\\n ;(async () => {\\n try {\\n const assembly = session.assemblyManager.get(assemblyName)\\n const w = +windowSize\\n if (Number.isNaN(w)) {\\n throw new Error(\'windowSize not a number\')\\n }\\n const { refName, pos, mateRefName, matePos } =\\n // @ts-expect-error\\n viewType.getBreakendCoveringRegions({ feature, assembly })\\n\\n const breakpointSplitView = session.addView(\\n \'BreakpointSplitView\',\\n {\\n type: \'BreakpointSplitView\',\\n displayName: `${\\n feature.get(\'name\') || feature.get(\'id\') || \'breakend\'\\n } split detail`,\\n views: [\\n {\\n type: \'LinearGenomeView\',\\n 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No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/4741.5a289f5d.chunk.js
--- a/x/static/js/4741.5a289f5d.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,2 +0,0 @@
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4741.5a289f5d.chunk.js.map
--- a/x/static/js/4741.5a289f5d.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4753.834007ba.chunk.js
--- a/x/static/js/4753.834007ba.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4753.834007ba.chunk.js.map
--- a/x/static/js/4753.834007ba.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4755.8d938db2.chunk.js
--- a/x/static/js/4755.8d938db2.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4755.8d938db2.chunk.js.map
--- a/x/static/js/4755.8d938db2.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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The name should match what\n is defined in the plugin's build.\n </DialogContentText>\n <TextField\n label=\"Plugin name\"\n variant=\"outlined\"\n value={umdPluginName}\n onChange={event => {\n setUMDPluginName(event.target.value)\n }}\n />\n <TextField\n label=\"Plugin URL\"\n variant=\"outlined\"\n value={umdPluginUrl}\n onChange={event => {\n setUMDPluginUrl(event.target.value)\n }}\n />\n <DialogContentText\n onClick={() => {\n setAdvancedOptionsOpen(!advancedOptionsOpen)\n }}\n >\n <IconButton\n className={cx(classes.expand, {\n [classes.expandOpen]: advancedOptionsOpen,\n })}\n aria-expanded={advancedOptionsOpen}\n aria-label=\"show more\"\n >\n <ExpandMoreIcon />\n </IconButton>\n Advanced options\n </DialogContentText>\n <Collapse in={advancedOptionsOpen}>\n <div className={classes.dialogContent}>\n <DialogContentText>\n The above fields assume that the plugin is built in UMD format.\n If your plugin is in another format, or you have additional\n builds you want to add (such as a CJS build for using NodeJS\n APIs in desktop), you can enter the URLs for those builds below.\n </DialogContentText>\n <TextField\n label=\"ESM build URL\"\n variant=\"outlined\"\n value={esmPluginUrl}\n onChange={event => {\n setESMPluginUrl(event.target.value)\n }}\n />\n <TextField\n label=\"CJS build URL\"\n variant=\"outlined\"\n value={cjsPluginUrl}\n onChange={event => {\n setCJSPluginUrl(event.target.value)\n }}\n />\n </div>\n </Collapse>\n </DialogContent>\n <DialogActions>\n <Button variant=\"contained\" onClick={onClose}>\n Cancel\n </Button>\n <Button\n variant=\"contained\"\n color=\"primary\"\n onClick={handleSubmit}\n disabled={!ready}\n >\n Submit\n </Button>\n </DialogActions>\n </form>\n </Dialog>\n )\n})\n\nexport default AddCustomPluginDialog\n"],"names":["useStyles","makeStyles","theme","dialogContent","display","flexDirection","expand","transform","marginLeft","transition","transitions","create","duration","shortest","expandOpen","observer","onClose","model","classes","cx","umdPluginName","setUMDPluginName","useState","umdPluginUrl","setUMDPluginUrl","esmPluginUrl","setESMPluginUrl","cjsPluginUrl","setCJSPluginUrl","advancedOptionsOpen","setAdvancedOptionsOpen","jbrowse","getSession","ready","Boolean","handleSubmit","addPlugin","name","umdUrl","esmUrl","cjsUrl","React","Dialog","open","title","onSubmit","DialogContent","className","DialogContentText","TextField","label","variant","value","onChange","event","target","onClick","IconButton","ExpandMoreIcon","Collapse","in","DialogActions","Button","color","disabled"],"sourceRoot":""}
\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/static/js/4770.3d757d6b.chunk.js
--- a/x/static/js/4770.3d757d6b.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,2 +0,0 @@
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-//# sourceMappingURL=4770.3d757d6b.chunk.js.map
\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/static/js/4770.3d757d6b.chunk.js.map
--- a/x/static/js/4770.3d757d6b.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4773.6cd74b80.chunk.js
--- a/x/static/js/4773.6cd74b80.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4773.6cd74b80.chunk.js.map
--- a/x/static/js/4773.6cd74b80.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/static/js/4806.7e497d7a.chunk.js
--- a/x/static/js/4806.7e497d7a.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,2 +0,0 @@
-"use strict";(globalThis.webpackChunk_jbrowse_web=globalThis.webpackChunk_jbrowse_web||[]).push([[4806],{74806:(e,t,a)=>{a.r(t),a.d(t,{default:()=>p});var n=a(7552),l=a(68446),o=a(29499),r=a(36715),s=a(33371),c=a(32808),i=a(1343),u=a(58507),d=a(5401),g=a(49823),f=a(36422),m=a(99546),h=a(20561);const p=(0,l.observer)((function(e){const{model:t,handleClose:a}=e,[l,p]=(0,n.useState)(""),[b,E]=(0,n.useState)(),[k,v]=(0,n.useState)(!1),[y,w]=(0,n.useState)(),[C,S]=(0,n.useState)(!0),A=/^[A-Za-z][A-Za-z0-9]$/.exec(l),T=2===l.length&&!A,$=(0,m.useDebounce)(l,1e3);return(0,n.useEffect)((()=>{(async()=>{try{if(!T){w(void 0),v(!0);const e=await(0,h.s_)({self:t,tag:$,blocks:(0,m.getContainingView)(t).staticBlocks});E(e)}}catch(e){console.error(e),w(e)}finally{v(!1)}})()}),[t,T,$]),n.createElement(g.Dialog,{open:!0,onClose:a,title:"Group by tag"},n.createElement(o.A,null,n.createElement(r.A,null,"Set the tag to group by. NOTE: this will make a set of fully functional subtracks with the filter by by default set to the values of the tag that are visible in the current view"),n.createElement(r.A,{color:"textSecondary"},"Examples: HP for haplotype, RG for read group, etc."),n.createElement(s.A,{control:n.createElement(c.A,{checked:C,onChange:()=>{S(!C)}}),label:"Make a new subtrack for undefined values of tag as well?"}),n.createElement(i.A,{value:l,onChange:e=>{p(e.target.value)},placeholder:"Enter tag name",inputProps:{maxLength:2,"data-testid":"group-tag-name-input"},error:T,helperText:T?"Not a valid tag":"",autoComplete:"off","data-testid":"group-tag-name"}),y?n.createElement(g.ErrorMessage,{error:y}):k?n.createElement(g.LoadingEllipses,{title:"Loading unique tags"}):b?n.createElement("div",null,n.createElement("div",null,"Found unique ",l," values:"),n.createElement("div",null,b.join(", "))):null),n.createElement(u.A,null,n.createElement(d.A,{variant:"contained",color:"primary",type:"submit",disabled:!b,autoFocus:!0,onClick:()=>{const e=(0,m.getContainingTrack)(t),n=(o=(0,f.getSnapshot)(e.configuration),JSON.parse(JSON.stringify(o)));var o;const r=(0,m.getSession)(t);if(b){const e=[...b];C&&e.push(void 0);for(const a of e){const e=r.addTrackConf({...n,trackId:`${n.trackId}-${l}:${a}-${+Date.now()}-sessionTrack`,name:`${n.name} ${l}:${a}`,displays:void 0});(0,m.getContainingView)(t).showTrack(e.trackId).displays[0].setFilterBy({flagInclude:0,flagExclude:1540,tagFilter:{tag:l,value:a}})}}a()}},"Submit"),n.createElement(d.A,{variant:"contained",color:"secondary",onClick:()=>{a()}},"Cancel")))}))}}]);
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4806.7e497d7a.chunk.js.map
--- a/x/static/js/4806.7e497d7a.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4861.6244e4c0.chunk.js
--- a/x/static/js/4861.6244e4c0.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4863.9dfed19c.chunk.js
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4864.28cfc358.chunk.js
--- a/x/static/js/4864.28cfc358.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4864.28cfc358.chunk.js.map
--- a/x/static/js/4864.28cfc358.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/489.43cb4a5f.chunk.js
--- a/x/static/js/489.43cb4a5f.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/489.43cb4a5f.chunk.js.map
--- a/x/static/js/489.43cb4a5f.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4902.452e575b.chunk.js
--- a/x/static/js/4902.452e575b.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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--- a/x/static/js/491.0011d1ad.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4947.2e80fd2d.chunk.js
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+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4947.2e80fd2d.chunk.js.map
--- a/x/static/js/4947.2e80fd2d.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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NativeSelect.propTypes /* remove-proptypes */ = {\n // ┌────────────────────────────── Warning ──────────────────────────────┐\n // │ These PropTypes are generated from the TypeScript type definitions. │\n // │ To update them, edit the d.ts file and run `pnpm proptypes`. │\n // └─────────────────────────────────────────────────────────────────────┘\n /**\n * The option elements to populate the select with.\n * Can be some `<option>` elements.\n */\n children: PropTypes.node,\n /**\n * Override or extend the styles applied to the component.\n * @default {}\n */\n classes: PropTypes.object,\n /**\n * @ignore\n */\n className: PropTypes.string,\n /**\n * The icon that displays the arrow.\n * @default ArrowDropDownIcon\n */\n IconComponent: PropTypes.elementType,\n /**\n * An `Input` element; does not have to be a material-ui specific `Input`.\n * @default <Input />\n */\n input: PropTypes.element,\n /**\n * [Attributes](https://developer.mozilla.org/en-US/docs/Web/HTML/Element/select#attributes) applied to the `select` element.\n */\n inputProps: PropTypes.object,\n /**\n * Callback fired when a menu item is selected.\n *\n * @param {React.ChangeEvent<HTMLSelectElement>} event The event source of the callback.\n * You can pull out the new value by accessing `event.target.value` (string).\n */\n onChange: PropTypes.func,\n /**\n * The system prop that allows defining system overrides as well as additional CSS styles.\n */\n sx: PropTypes.oneOfType([PropTypes.arrayOf(PropTypes.oneOfType([PropTypes.func, PropTypes.object, PropTypes.bool])), PropTypes.func, PropTypes.object]),\n /**\n * The `input` value. 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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4974.cf97ef5b.chunk.js
--- a/x/static/js/4974.cf97ef5b.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/4974.cf97ef5b.chunk.js.map
--- a/x/static/js/4974.cf97ef5b.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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flex item properties to be used to lay out the children.\\n */\\n children: PropTypes.node,\\n /**\\n * Override or extend the styles applied to the component.\\n */\\n classes: PropTypes.object,\\n /**\\n * @ignore\\n */\\n className: PropTypes.string,\\n /**\\n * The component used for the root node.\\n * Either a string to use a HTML element or a component.\\n */\\n component: PropTypes.elementType,\\n /**\\n * If `true`, disables gutter padding.\\n * @default false\\n */\\n disableGutters: PropTypes.bool,\\n /**\\n * The system prop that allows defining system overrides as well as additional CSS styles.\\n */\\n sx: PropTypes.oneOfType([PropTypes.arrayOf(PropTypes.oneOfType([PropTypes.func, PropTypes.object, PropTypes.bool])), PropTypes.func, PropTypes.object]),\\n /**\\n * The variant to use.\\n * @default \'regular\'\\n */\\n variant: PropTypes /* @typescript-to-proptypes-ignore */.oneOfType([PropTypes.oneOf([\'dense\', \'regular\']), PropTypes.string])\\n} : void 0;\\nexport default Toolbar;","import generateUtilityClasses from \'@mui/utils/generateUtilityClasses\';\\nimport generateUtilityClass from \'@mui/utils/generateUtilityClass\';\\nexport function getToolbarUtilityClass(slot) {\\n return generateUtilityClass(\'MuiToolbar\', slot);\\n}\\nconst toolbarClasses = generateUtilityClasses(\'MuiToolbar\', [\'root\', \'gutters\', \'regular\', \'dense\']);\\nexport default toolbarClasses;"],"names":["circularRotateKeyframe","circularDashKeyframe","rotateAnimation","dashAnimation","CircularProgressRoot","name","slot","overridesResolver","props","styles","ownerState","root","variant","color","theme","display","variants","style","transition","transitions","create","animation","Object","entries","palette","filter","map","vars","main","CircularProgressSVG","svg","CircularProgressCircle","circle","disableShrink","circleDisableShrink","stroke","strokeDasharray","strokeDashoffset","inProps","ref","className","size","thickness","value","other","classes","slots","useUtilityClasses","circleStyle","rootStyle","rootProps","circumference","Math","PI","toFixed","round","transform","width","height","role","children","viewBox","cx","cy","r","fill","strokeWidth","getCircularProgressUtilityClass","mapEventPropToEvent","eventProp","substring","toLowerCase","ClickAwayListener","disableReactTree","mouseEvent","onClickAway","touchEvent","movedRef","nodeRef","activatedRef","syntheticEventRef","setTimeout","current","handleRef","handleClickAway","event","insideReactTree","doc","documentElement","clientWidth","clientX","clientHeight","clientY","clickedRootScrollbar","insideDOM","composedPath","includes","contains","target","createHandleSynthetic","handlerName","childrenPropsHandler","childrenProps","mappedTouchEvent","handleTouchMove","addEventListener","removeEventListener","mappedMouseEvent","ToolbarRoot","disableGutters","gutters","position","alignItems","paddingLeft","spacing","paddingRight","breakpoints","up","minHeight","mixins","toolbar","component","as","getToolbarUtilityClass"],"sourceRoot":""}\n\\ No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/5031.6eccfd35.chunk.js
--- a/x/static/js/5031.6eccfd35.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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--- a/x/static/js/5090.bc77ac67.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5099.14f82444.chunk.js
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5099.14f82444.chunk.js.LICENSE.txt
--- a/x/static/js/5099.14f82444.chunk.js.LICENSE.txt Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,12 +0,0 @@
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-/*!
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5099.14f82444.chunk.js.map
--- a/x/static/js/5099.14f82444.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5132.00a31df0.chunk.js
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5132.00a31df0.chunk.js.map
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(\\n <PairLink model={model} locString={value as string} />\\n ) : (\\n <Formatter value={value} />\\n )\\n }\\n />\\n {SA !== undefined ? (\\n <SupplementaryAlignments model={model} tag={SA} feature={feat} />\\n ) : null}\\n {flags & 1 ? 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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5156.75195722.chunk.js
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--- a/x/static/js/5189.3e22269d.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5255.af554ced.chunk.js.LICENSE.txt
--- a/x/static/js/5255.af554ced.chunk.js.LICENSE.txt Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5255.af554ced.chunk.js.map
--- a/x/static/js/5255.af554ced.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5260.e7b7aeb6.chunk.js
--- a/x/static/js/5260.e7b7aeb6.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5260.e7b7aeb6.chunk.js.map
--- a/x/static/js/5260.e7b7aeb6.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5327.8f1dcfc1.chunk.js
--- a/x/static/js/5327.8f1dcfc1.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5331.28d667f0.chunk.js
--- a/x/static/js/5331.28d667f0.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5331.28d667f0.chunk.js.map
--- a/x/static/js/5331.28d667f0.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5369.993afa3f.chunk.js
--- a/x/static/js/5369.993afa3f.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5369.993afa3f.chunk.js.map
--- a/x/static/js/5369.993afa3f.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/static/js/5461.5c8cf5d1.chunk.js
--- a/x/static/js/5461.5c8cf5d1.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/static/js/5461.5c8cf5d1.chunk.js.map
--- a/x/static/js/5461.5c8cf5d1.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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--- a/x/static/js/5484.3ceeebff.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5484.3ceeebff.chunk.js.map
--- a/x/static/js/5484.3ceeebff.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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flex item properties to be used to lay out the children.\\n */\\n children: PropTypes.node,\\n /**\\n * Override or extend the styles applied to the component.\\n */\\n classes: PropTypes.object,\\n /**\\n * @ignore\\n */\\n className: PropTypes.string,\\n /**\\n * The component used for the root node.\\n * Either a string to use a HTML element or a component.\\n */\\n component: PropTypes.elementType,\\n /**\\n * If `true`, disables gutter padding.\\n * @default false\\n */\\n disableGutters: PropTypes.bool,\\n /**\\n * The system prop that allows defining system overrides as well as additional CSS styles.\\n */\\n sx: PropTypes.oneOfType([PropTypes.arrayOf(PropTypes.oneOfType([PropTypes.func, PropTypes.object, PropTypes.bool])), PropTypes.func, PropTypes.object]),\\n /**\\n * The variant to use.\\n * @default \'regular\'\\n */\\n variant: PropTypes /* @typescript-to-proptypes-ignore */.oneOfType([PropTypes.oneOf([\'dense\', \'regular\']), PropTypes.string])\\n} : void 0;\\nexport 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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5511.154ce441.chunk.js
--- a/x/static/js/5511.154ce441.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5515.671905b2.chunk.js
--- a/x/static/js/5515.671905b2.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5595.b4517d69.chunk.js
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5595.b4517d69.chunk.js.LICENSE.txt
--- a/x/static/js/5595.b4517d69.chunk.js.LICENSE.txt Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,7 +0,0 @@
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- *
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- */

diff -r cec274db51c0 -r ed3a21033188 x/static/js/5595.b4517d69.chunk.js.map
--- a/x/static/js/5595.b4517d69.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5608.1b8d39e1.chunk.js
--- a/x/static/js/5608.1b8d39e1.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/561.8b38948f.chunk.js
--- a/x/static/js/561.8b38948f.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/561.8b38948f.chunk.js.map
--- a/x/static/js/561.8b38948f.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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`rgba(${theme.vars.palette.primary.mainChannel} / ${theme.vars.palette.action.selectedOpacity})` : alpha(theme.palette.primary.main, theme.palette.action.selectedOpacity),\n '&:hover': {\n backgroundColor: theme.vars ? `rgba(${theme.vars.palette.primary.mainChannel} / calc(${theme.vars.palette.action.selectedOpacity} + ${theme.vars.palette.action.hoverOpacity}))` : alpha(theme.palette.primary.main, theme.palette.action.selectedOpacity + theme.palette.action.hoverOpacity)\n }\n }\n})));\nconst defaultComponent = 'tr';\n/**\n * Will automatically set dynamic row height\n * based on the material table element parent (head, body, etc).\n */\nconst TableRow = /*#__PURE__*/React.forwardRef(function TableRow(inProps, ref) {\n const props = useDefaultProps({\n props: inProps,\n name: 'MuiTableRow'\n });\n const {\n className,\n component = defaultComponent,\n hover = false,\n selected = false,\n ...other\n } = props;\n const tablelvl2 = React.useContext(Tablelvl2Context);\n const ownerState = {\n ...props,\n component,\n hover,\n selected,\n head: tablelvl2 && tablelvl2.variant === 'head',\n footer: tablelvl2 && tablelvl2.variant === 'footer'\n };\n const classes = useUtilityClasses(ownerState);\n return /*#__PURE__*/_jsx(TableRowRoot, {\n as: component,\n ref: ref,\n className: clsx(classes.root, className),\n role: component === defaultComponent ? 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--- a/x/static/js/5640.33b8306c.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5668.73016b9c.chunk.js
--- a/x/static/js/5668.73016b9c.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5668.73016b9c.chunk.js.map
--- a/x/static/js/5668.73016b9c.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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--- a/x/static/js/5676.818528e8.chunk.js Fri Oct 18 11:57:55 2024 +0000
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--- a/x/static/js/5676.818528e8.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5677.28a25579.chunk.js
--- a/x/static/js/5677.28a25579.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5677.28a25579.chunk.js.map
--- a/x/static/js/5677.28a25579.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5682.ea285a50.chunk.js
--- a/x/static/js/5682.ea285a50.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5682.ea285a50.chunk.js.map
--- a/x/static/js/5682.ea285a50.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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i < cigar.length; i++) {\\n const len = +cigar[i]!\\n const op = cigar[i + 1]!\\n const min = Math.min(len, startX - featX)\\n\\n if (featX >= startX) {\\n break\\n }\\n if (op === \'I\') {\\n mateX'..b'l1, featAsm),\\n view2.views[1]!.navToLocString(l2, mateAsm),\\n ])\\n}\\n","import React, { useState } from \'react\'\\nimport { Dialog } from \'@jbrowse/core/ui\'\\nimport { Feature, getSession } from \'@jbrowse/core/util\'\\nimport {\\n Button,\\n Checkbox,\\n DialogActions,\\n DialogContent,\\n FormControlLabel,\\n TextField,\\n} from \'@mui/material\'\\nimport { navToSynteny } from \'./util\'\\nimport { makeStyles } from \'tss-react/mui\'\\n\\nconst useStyles = makeStyles()({\\n padding: {\\n margin: 10,\\n border: \'1px solid #ccc\',\\n },\\n})\\n\\nexport default function LaunchSyntenyViewDialog({\\n model,\\n feature,\\n handleClose,\\n}: {\\n model: unknown\\n feature: Feature\\n handleClose: () => void\\n}) {\\n const { classes } = useStyles()\\n const inverted = feature.get(\'strand\') === -1\\n const [horizontallyFlip, setHorizontallyFlip] = useState(inverted)\\n const [windowSize, setWindowSize] = useState(\'1000\')\\n return (\\n <Dialog open title=\\"Launch synteny view\\" onClose={handleClose}>\\n <DialogContent>\\n {inverted ? (\\n <FormControlLabel\\n className={classes.padding}\\n control={\\n <Checkbox\\n checked={horizontallyFlip}\\n onChange={event => {\\n setHorizontallyFlip(event.target.checked)\\n }}\\n />\\n }\\n label=\\"Note: The feature is inverted in orientation on the target\\n sequence. This will result in the lower panel having genomic\\n coordinates decreasing left to right. Horizontally flip?\\"\\n />\\n ) : null}\\n <TextField\\n label=\\"Add window size in bp\\"\\n value={windowSize}\\n onChange={event => {\\n setWindowSize(event.target.value)\\n }}\\n />\\n </DialogContent>\\n <DialogActions>\\n <Button\\n variant=\\"contained\\"\\n onClick={() => {\\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\\n ;(async () => {\\n try {\\n await navToSynteny({\\n feature,\\n windowSize: +windowSize,\\n horizontallyFlip,\\n model,\\n })\\n } catch (e) {\\n console.error(e)\\n getSession(model).notifyError(`${e}`, e)\\n }\\n })()\\n handleClose()\\n }}\\n >\\n Submit\\n </Button>\\n <Button\\n variant=\\"contained\\"\\n color=\\"secondary\\"\\n onClick={() => {\\n handleClose()\\n }}\\n >\\n Cancel\\n </Button>\\n </DialogActions>\\n </Dialog>\\n )\\n}\\n"],"names":["parseCigar","MismatchParser","f","n","Math","floor","findPosInCigar","cigar","startX","featX","mateX","i","length","len","op","min","useStyles","makeStyles","padding","margin","border","LaunchSyntenyViewDialog","model","feature","handleClose","classes","inverted","get","horizontallyFlip","setHorizontallyFlip","useState","windowSize","setWindowSize","React","Dialog","open","title","onClose","DialogContent","FormControlLabel","className","control","Checkbox","checked","onChange","event","target","label","TextField","value","DialogActions","Button","variant","onClick","async","ws","session","getSession","track","getContainingTrack","reg","getContainingView","dynamicBlocks","contentBlocks","Error","strand","regStart","start","regEnd","end","featStart","featEnd","mate","mateStart","mateEnd","mateAsm","assemblyName","mateRef","refName","featAsm","featRef","rMateStart","rMateEnd","rFeatStart","rFeatEnd","p","fStartX","mStartX","fEndX","mEndX","flipper","trackId","configuration","view2","addView","type","views","id","random","hideHeader","tracks","displays","l1","m1","m2","max","l2","Promise","all","navToLocString","navToSynteny","e","console","error","notifyError","color"],"sourceRoot":""}\n\\ No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/5727.f7a524b6.chunk.js
--- a/x/static/js/5727.f7a524b6.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5727.f7a524b6.chunk.js.map
--- a/x/static/js/5727.f7a524b6.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5736.48705208.chunk.js
--- a/x/static/js/5736.48705208.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5736.48705208.chunk.js.map
--- a/x/static/js/5736.48705208.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5746.39e4296b.chunk.js
--- a/x/static/js/5746.39e4296b.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5746.39e4296b.chunk.js.map
--- a/x/static/js/5746.39e4296b.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5763.48010c9a.chunk.js.map
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5896.622b5e88.chunk.js
--- a/x/static/js/5896.622b5e88.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5896.622b5e88.chunk.js.map
--- a/x/static/js/5896.622b5e88.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
-{"version":3,"file":"static/js/5896.622b5e88.chunk.js","mappings":"2NAYA,MA4CA,GA5C+BA,E,SAAAA,WAAS,UAAgC,oBACtEC,EAAmB,QACnBC,EAAO,YACPC,IASA,MAAM,eAAEC,EAAc,KAAEC,GAASJ,EACjC,OACEK,EAAAA,cAACC,EAAAA,OAAM,CAACC,MAAI,EAACC,MAAO,sBAAsBJ,MACxCC,EAAAA,cAACI,EAAAA,EAAa,KACZJ,EAAAA,cAACK,EAAAA,EAAiB,KAAC,qDAIrBL,EAAAA,cAACM,EAAAA,EAAa,KACZN,EAAAA,cAACO,EAAAA,EAAM,CACLC,QAASA,KACPX,GAAa,EAEfY,MAAM,WACP,UAGDT,EAAAA,cAACO,EAAAA,EAAM,CACLG,QAAQ,YACRD,MAAM,UACND,QAASA,KACPZ,EAAQe,mBAAmBb,GAC3BD,GAAa,GAEhB,OAMT,G","sources":["../../../plugins/data-management/src/HierarchicalTrackSelectorWidget/components/dialogs/DeleteConnectionDialog.tsx"],"sourcesContent":["import React from 'react'\nimport {\n DialogContent,\n DialogContentText,\n DialogActions,\n Button,\n} from '@mui/material'\nimport { Dialog } from '@jbrowse/core/ui'\nimport { observer } from 'mobx-react'\nimport { AnyConfigurationModel } from '@jbrowse/core/configuration'\nimport { AbstractSessionModel } from '@jbrowse/core/util'\n\nconst DeleteConnectionDialog = observer(function DeleteConnectionDialog({\n deleteDialogDetails,\n session,\n handleClose,\n}: {\n deleteDialogDetails: {\n name: string\n connectionConf: AnyConfigurationModel\n }\n session: AbstractSessionModel\n handleClose: () => void\n}) {\n const { connectionConf, name } = deleteDialogDetails\n return (\n <Dialog open title={`Delete connection \"${name}\"`}>\n <DialogContent>\n <DialogContentText>\n Are you sure you want to delete this connection?\n </DialogContentText>\n </DialogContent>\n <DialogActions>\n <Button\n onClick={() => {\n handleClose()\n }}\n color=\"primary\"\n >\n Cancel\n </Button>\n <Button\n variant=\"contained\"\n color=\"primary\"\n onClick={() => {\n session.deleteConnection?.(connectionConf)\n handleClose()\n }}\n >\n OK\n </Button>\n </DialogActions>\n </Dialog>\n )\n})\n\nexport default DeleteConnectionDialog\n"],"names":["observer","deleteDialogDetails","session","handleClose","connectionConf","name","React","Dialog","open","title","DialogContent","DialogContentText","DialogActions","Button","onClick","color","variant","deleteConnection"],"sourceRoot":""}
\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/static/js/5903.9145cef7.chunk.js
--- a/x/static/js/5903.9145cef7.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5903.9145cef7.chunk.js.map
--- a/x/static/js/5903.9145cef7.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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onChange={event => {\\n setCopyTracks(event.target.checked)\\n }}\\n />\\n\\n <TextField\\n label=\\"Window size (bp)\\"\\n value={windowSize}\\n onChange={event => {\\n setWindowSize(event.target.value)\\n }}\\n />\\n </DialogContent>\\n <DialogActions>\\n <Button\\n onClick={() => {\\n const session = getSession(model)\\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\\n ;(async () => {\\n try {\\n const assembly = session.assemblyManager.get(assemblyName)\\n const w = +windowSize\\n if (Number.isNaN(w)) {\\n throw new Error(\'windowSize not a number\')\\n }\\n const { refName, pos, mateRefName, matePos } =\\n // @ts-expect-error\\n viewType.getBreakendCoveringRegions({ feature, assembly })\\n\\n const breakpointSplitView = session.addView(\\n \'BreakpointSplitView\',\\n {\\n type: \'BreakpointSplitView\',\\n displayName: `${\\n feature.get(\'name\') || feature.get(\'id\') || \'breakend\'\\n } split detail`,\\n views: [\\n {\\n type: \'LinearGenomeView\',\\n tracks: stripIds(getSnapshot(view.tracks)),\\n },\\n ],\\n },\\n ) as unknown as { views: LinearGenomeViewModel[] }\\n\\n await breakpointSplitView.views[0]!.navToLocations(\\n gatherOverlaps(\\n [\\n {\\n refName,\\n start: Math.max(0, pos - w),\\n end: pos + w,\\n assemblyName,\\n },\\n {\\n refName: mateRefName,\\n start: Math.max(0, matePos - w),\\n end: matePos + w,\\n assemblyName,\\n },\\n ],\\n w,\\n ),\\n )\\n } catch (e) {\\n console.error(e)\\n session.notify(`${e}`)\\n }\\n })()\\n handleClose()\\n }}\\n variant=\\"contained\\"\\n color=\\"primary\\"\\n autoFocus\\n >\\n OK\\n </Button>\\n <Button\\n color=\\"secondary\\"\\n variant=\\"contained\\"\\n onClick={() => {\\n handleClose()\\n }}\\n >\\n Cancel\\n </Button>\\n </DialogActions>\\n </Dialog>\\n )\\n})\\n\\nexport default BreakendSingleLevelOptionDialog\\n"],"names":["useStyles","makeStyles","block","display","Checkbox2","checked","disabled","label","onChange","classes","React","FormControlLabel","className","control","Checkbox","stripIds","arr","map","id","displays","rest","observer","model","handleClose","feature","assemblyName","viewType","view","copyTracks","setCopyTracks","useState","mirror","setMirror","Dialog","open","onClose","title","DialogContent","event","target","DialogActions","Button","onClick","session","getSession","asm","assemblyManager","waitForAssembly","Error","refName","pos","mateRefName","matePos","getBreakendCoveringRegions","assembly","viewTracks","getSnapshot","tracks","breakpointSplitView","addView","type","displayName","get","views","hideHeader","reverse","r1","regions","find","r","r2","Promise","all","navToLocations","start","end","when","initialized","zoomTo","centerAt","e","console","error","notify","variant","color","autoFocus","windowSize","setWindowSize","useLocalStorage","TextField","value","w","Number","isNaN","gatherOverlaps","Math","max"],"sourceRoot":""}\n\\ No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/5904.240caa72.chunk.js
--- a/x/static/js/5904.240caa72.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,2 +0,0 @@\n-"use strict";(globalThis.webpackChunk_jbrowse_web=globalThis.webpackChunk_jbrowse_web||[]).push([[5904,7706],{35904:(e,t,n)=>{n.r(t),n.d(t,{default:()=>p});var r=n(46377),a=n(32595),s=n(99834),o=n(66885),i=n(99546),c=n(68584),l=n(7706),h=n(82727),d=n(72147),u=n(78054);function f(e){const[t,n]=e.reduce((([e,t],[n,r])=>[e+n*r,t+r]),[0,0]);return t/n}const{parseCigar:m}=h.aF;class p extends r.BaseFeatureDataAdapter{static capabilities=["getFeatures","getRefNames"];async setup(e){return this.setupP||(this.setupP=this.setupPre(e).catch((e=>{throw this.setupP=void 0,e}))),this.setupP}async setupPre(e){const t=this.pluginManager,n=(0,s.openLocation)(this.getConf("pafLocation"),t),r=await n.readFile(e),a=(0,i.isGzip)(r)?await(0,l.unzip)(r):r;return(0,u.PX)(a,u.xI)}async hasDataForRefName(){return!0}getAssemblyNames(){const e=this.getConf("assemblyNames");return 0===e.length?[this.getConf("queryAssembly"),this.getConf("targetAssembly")]:e}async getRefNames(e={}){const 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o=this.getAssemblyNames(),{start:i,end:l,refName:h,assemblyName:p}=e,g=o.indexOf(p),w=0===g;-1===g&&(console.warn(`${p} not found in this adapter`),n.complete());for(let e=0;e<r.length;e++){const t=r[e];let s=0,c=0,f="",g="",b=0,y=0;w?(s=t.qstart,c=t.qend,f=t.qname,g=t.tname,b=t.tstart,y=t.tend):(s=t.tstart,c=t.tend,f=t.tname,g=t.qname,b=t.qstart,y=t.qend);const{extra:x,strand:k}=t;if(f===h&&(0,a.R6)(i,l,s,c)){const{numMatches:t=0,blockLen:r=1,cg:a,...i}=x;let l=x.cg;x.cg&&(w&&-1===k?l=(0,u.qm)(m(x.cg)).join(""):w&&(l=(0,u.gJ)(x.cg))),n.next(new d.A({uniqueId:e+p,assemblyName:p,start:s,end:c,type:"match",refName:f,strand:k,...i,CIGAR:l,syntenyId:e,identity:t/r,numMatches:t,blockLen:r,mate:{start:b,end:y,refName:g,assemblyName:o[+w]}}))}}n.complete()}))}freeResources(){}}},72147:(e,t,n)=>{n.d(t,{A:()=>o});var r=n(99546),a=n(82727);const{getMismatches:s}=a.aF;class o extends 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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5904.240caa72.chunk.js.map
--- a/x/static/js/5904.240caa72.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5930.0ffd2546.chunk.js
--- a/x/static/js/5930.0ffd2546.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5930.0ffd2546.chunk.js.map
--- a/x/static/js/5930.0ffd2546.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/5951.251be759.chunk.js
--- a/x/static/js/5951.251be759.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5951.251be759.chunk.js.map
--- a/x/static/js/5951.251be759.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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RadioGroup.propTypes /* remove-proptypes */ = {\n // ┌────────────────────────────── Warning ──────────────────────────────┐\n // │ These PropTypes are generated from the TypeScript type definitions. │\n // │ To update them, edit the d.ts file and run `pnpm proptypes`. │\n // └─────────────────────────────────────────────────────────────────────┘\n /**\n * The content of the component.\n */\n children: PropTypes.node,\n /**\n * @ignore\n */\n className: PropTypes.string,\n /**\n * The default value. Use when the component is not controlled.\n */\n defaultValue: PropTypes.any,\n /**\n * The name used to reference the value of the control.\n * If you don't provide this prop, it falls back to a randomly generated name.\n */\n name: PropTypes.string,\n /**\n * Callback fired when a radio button is selected.\n *\n * @param {React.ChangeEvent<HTMLInputElement>} event The event source of the callback.\n * @param {string} value The value of the selected radio button.\n * You can pull out the new value by accessing `event.target.value` (string).\n */\n onChange: PropTypes.func,\n /**\n * Value of the selected radio button. 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diff -r cec274db51c0 -r ed3a21033188 x/static/js/596.84c38eb7.chunk.js
--- a/x/static/js/596.84c38eb7.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/596.84c38eb7.chunk.js.map
--- a/x/static/js/596.84c38eb7.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5998.22bd8296.chunk.js
--- a/x/static/js/5998.22bd8296.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/5998.22bd8296.chunk.js.map
--- a/x/static/js/5998.22bd8296.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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jb2Features,\\n }\\n jb2TrackConfig.type = \'FeatureTrack\'\\n return jb2TrackConfig\\n}\\n\\nexport async function createRefSeqsAdapter(\\n refSeqs: string | RefSeqs,\\n): Promise<Jb2Adapter> {\\n if (typeof refSeqs === \'string\') {\\n // assume refSeqs is a url if it is string\\n refSeqs = {\\n url: refSeqs,\\n }\\n }\\n\\n // check refseq urls\\n if (refSeqs.url) {\\n if (/.fai$/.exec(refSeqs.url)) {\\n return {\\n type: \'IndexedFastaAdapter\',\\n fastaLocation: {\\n uri: refSeqs.url.slice(0, -4),\\n locationType: \'UriLocation\',\\n },\\n faiLocation: {\\n uri: refSeqs.url,\\n locationType: \'UriLocation\',\\n },\\n }\\n }\\n if (/.2bit$/.exec(refSeqs.url)) {\\n return {\\n type: \'TwoBitAdapter\',\\n twoBitLocation: { uri: refSeqs.url, locationType: \'UriLocation\' },\\n }\\n }\\n if (/.fa$/.exec(refSeqs.url)) {\\n throw new Error(\'Unindexed FASTA adapter not available\')\\n }\\n if (/.sizes/.exec(refSeqs.url)) {\\n throw new Error(\'chromosome SIZES adapter not available\')\\n 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}\\n}\\n"],"names":["convertTrackConfig","jb1TrackConfig","dataRoot","sequenceAdapter","jb2TrackConfig","trackId","objectHash","name","key","label","description","metadata","Description","category","split","storeClass","urlTemplate","endsWith","trackIdentifier","console","warn","generateUnsupportedTrackConf","jb2Features","features","map","feature","jb2Feature","JSON","parse","stringify","refName","seq_id","uniqueId","start","end","adapter","type","generateFromConfigTrackConfig","resolveUrlTemplate","URL","href","replaceAll","bamLocation","uri","locationType","baiUrlTemplate","index","location","csiUrlTemplate","indexType","cramLocation","craiLocation","craiUrlTemplate","rootUrlTemplate","defaultRendering","bigWigLocation","vcfGzLocation","tbiUrlTemplate","gffLocation","bigBedLocation","gffGzLocation","bedGzLocation","gtfLocation","fastaLocation","faiLocation","faiUrlTemplate","gziLocation","gziUrlTemplate","twoBitLocation","guessAdapter","undefined","UNSUPPORTED","UNKNOWN","generateUnknownTrackConf","guessTrackType"],"sourceRoot":""}\n\\ No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/6021.21769087.chunk.js
--- a/x/static/js/6021.21769087.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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-"use strict";(globalThis.webpackChunk_jbrowse_web=globalThis.webpackChunk_jbrowse_web||[]).push([[6021],{96021:(e,t,r)=>{r.r(t),r.d(t,{Tooltip:()=>o.A,default:()=>m});var n=r(7552),l=r(68446),a=r(75429),o=r(88262);function c(){return c=Object.assign?Object.assign.bind():function(e){for(var t=1;t<arguments.length;t++){var r=arguments[t];for(var n in r)({}).hasOwnProperty.call(r,n)&&(e[n]=r[n])}return e},c.apply(null,arguments)}const s=e=>e.toLocaleString("en-US"),u=n.forwardRef((function({model:e,feature:t},r){const l=t.get("start"),o=t.get("end"),c=t.get("refName"),u=l===o?s(l):`${s(l)}..${s(o)}`,m=t.get("sources"),i=t.get("source"),b=t.get("summary"),g=Object.fromEntries(e.sources.map((e=>[e.name,e])));return n.createElement("div",{ref:r},[c,u].filter((e=>!!e)).join(":"),n.createElement("br",null),m?n.createElement("table",null,n.createElement("thead",null,n.createElement("tr",null,n.createElement("th",null,"color"),n.createElement("th",null,"source"),n.createElement("th",null,"score"))),n.createElement("tbody",null,Object.entries(m).map((([e,t])=>n.createElement("tr",{key:e},n.createElement("td",{style:{background:g[e].color}}," "),n.createElement("td",null,e),n.createElement("td",null,(0,a.toP)(t.score))))))):n.createElement("span",null,i," ",b?`min:${(0,a.toP)(t.get("minScore"))} avg:${(0,a.toP)(t.get("score"))} max:${(0,a.toP)(t.get("maxScore"))}`:(0,a.toP)(t.get("score"))))})),m=(0,l.observer)((e=>n.createElement(o.A,c({useClientY:!0,TooltipContents:u},e))))}}]);
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/6021.21769087.chunk.js.map
--- a/x/static/js/6021.21769087.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/static/js/6043.e402bf73.chunk.js
--- a/x/static/js/6043.e402bf73.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,2 +0,0 @@
-"use strict";(globalThis.webpackChunk_jbrowse_web=globalThis.webpackChunk_jbrowse_web||[]).push([[6043],{8424:(e,t,a)=>{a.r(t),a.d(t,{default:()=>m});var r=a(7552),o=a(68446),l=a(29499),n=a(36715),c=a(1343),s=a(58507),i=a(5401),d=a(49823);const m=(0,o.observer)((function({model:e,handleClose:t}){const[a,o]=(0,r.useState)(""),m=/^[A-Za-z][A-Za-z0-9]$/.exec(a);return r.createElement(d.Dialog,{open:!0,onClose:t,title:"Color by tag"},r.createElement(l.A,{style:{overflowX:"hidden"}},r.createElement(n.A,null,"Enter tag to color by: "),r.createElement(n.A,{color:"textSecondary"},"Examples: XS or TS for RNA-seq inferred read strand, ts (lower-case) for minimap2 read strand, HP for haplotype, RG for read group, etc."),r.createElement(c.A,{value:a,onChange:e=>{o(e.target.value)},placeholder:"Enter tag name",inputProps:{maxLength:2},error:2===a.length&&!m,helperText:2!==a.length||m?"":"Not a valid tag",autoComplete:"off"}),r.createElement(s.A,null,r.createElement(i.A,{variant:"contained",color:"primary",onClick:()=>{e.setColorScheme({type:"tag",tag:a}),t()},disabled:!m},"Submit"),r.createElement(i.A,{variant:"contained",color:"secondary",onClick:t},"Cancel"))))}))}}]);
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/6043.e402bf73.chunk.js.map
--- a/x/static/js/6043.e402bf73.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/6054.e0881c55.chunk.js
--- a/x/static/js/6054.e0881c55.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/6054.e0881c55.chunk.js.map
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PropTypes.oneOf([\'horizontal\', \'vertical\']),\\n /**\\n * The system prop that allows defining system overrides as well as additional CSS styles.\\n */\\n sx: PropTypes.oneOfType([PropTypes.arrayOf(PropTypes.oneOfType([PropTypes.func, PropTypes.object, PropTypes.bool])), PropTypes.func, PropTypes.object])\\n} : void 0;\\nexport default Stepper;","import * as React from \'react\';\\n/**\\n * Provides information about the current step in Stepper.\\n */\\nconst StepperContext = /*#__PURE__*/React.createContext({});\\nif (process.env.NODE_ENV !== \'production\') {\\n StepperContext.displayName = \'StepperContext\';\\n}\\n\\n/**\\n * Returns the current StepperContext or an empty object if no StepperContext\\n * has been defined in the component tree.\\n */\\nexport function useStepperContext() {\\n return React.useContext(StepperContext);\\n}\\nexport default StepperContext;","import generateUtilityClasses from \'@mui/utils/generateUtilityClasses\';\\nimport generateUtilityClass from 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diff -r cec274db51c0 -r ed3a21033188 x/static/js/6149.c6c4af73.chunk.js
--- a/x/static/js/6149.c6c4af73.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/6235.93768761.chunk.js
--- a/x/static/js/6235.93768761.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/6235.93768761.chunk.js.map
--- a/x/static/js/6235.93768761.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/6310.ae82dc58.chunk.js
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e=g.length;a[s++]={start:n,type:"softclip",base:`S${e}`,cliplen:e,length:1}}else if("P"===h);else if("H"===h){const e=g;a[s++]={start:n,type:"hardclip",base:`H${e}`,cliplen:e,length:1}}else"D"===h?a[s++]={type:"deletion",length:g,start:n,base:"*"}:"b"===h||"q"===h'..b'+]={start:n,type:"insertion",base:`${i}`,length:0},i=0),a.slice(0,s)}(e,this.get("start"),t)}}class u extends s.BaseFeatureDataAdapter{samHeader={};seqIdToOriginalRefName=[];async configurePre(){const e=this.getConf("cramLocation"),t=this.getConf("craiLocation"),r=this.pluginManager,s=new a.bQ({cramFilehandle:(0,n.openLocation)(e,r),index:new a.Wb({filehandle:(0,n.openLocation)(t,r)}),seqFetch:(...e)=>this.seqFetch(...e),checkSequenceMD5:!1});if(!this.getSubAdapter)throw new Error("Error getting subadapter");const i=this.getConf("sequenceAdapter");if(!i)throw new Error("no sequenceAdapter supplied to CramAdapter config");return{cram:s,sequenceAdapter:(await this.getSubAdapter(i)).dataAdapter}}async configure(){return this.configureP||(this.configureP=this.configurePre().catch((e=>{throw this.configureP=void 0,e}))),this.configureP}async getHeader(e){const{cram:t}=await this.configure();return t.cram.getHeaderText()}async seqFetch(e,t,r){t-=1;const{sequenceAdapter:a}=await this.configure(),s=this.refIdToOriginalName(e)||this.refIdToName(e);if(!s)throw new Error("unknown");const n=(await(0,d._)(a.getFeatures({refName:s,start:t,end:r,assemblyName:""}).pipe((0,c.$)()))).sort(((e,t)=>e.get("start")-t.get("start"))).map((e=>{const a=e.get("start"),s=e.get("end"),i=Math.max(t-a,0),n=Math.min(r-a,s-a)-i;return(e.get("seq")||e.get("residues")).slice(i,i+n)})).join(""),o=r-t;if(n.length!==o)throw new Error(`fetching ${s}:${(0,i.toLocale)(t-1)}-${(0,i.toLocale)(r)} returned ${(0,i.toLocale)(n.length)} bases, should have returned ${(0,i.toLocale)(o)}`);return n}async setupPre(e){const{statusCallback:t=()=>{}}=e||{};return(0,i.updateStatus)("Downloading index",t,(async()=>{const e=await this.configure(),{cram:t}=e,r=await t.cram.getSamHeader(),a=[],s={};r.filter((e=>"SQ"===e.tag)).forEach(((e,t)=>{const r=e.data.find((e=>"SN"===e.tag));if(r){const e=r.value;s[e]=t,a[t]=e}}));const i=r.filter((e=>"RG"===e.tag)).map((e=>e.data.find((e=>"ID"===e.tag))?.value)),n={idToName:a,nameToId:s,readGroups:i};return this.samHeader=n,{samHeader:n,...e}}))}async setup(e){return this.setupP||(this.setupP=this.setupPre(e).catch((e=>{throw this.setupP=void 0,e}))),this.setupP}async getRefNames(e){const{samHeader:t}=await this.setup(e);if(!t.idToName)throw new Error("CRAM file has no header lines");return t.idToName}refNameToId(e){return this.samHeader.nameToId?this.samHeader.nameToId[e]:this.seqIdToRefName?this.seqIdToRefName.indexOf(e):void 0}refIdToName(e){return this.samHeader.idToName?.[e]||this.seqIdToRefName?.[e]}refIdToOriginalName(e){return 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diff -r cec274db51c0 -r ed3a21033188 x/static/js/6391.aabba4a1.chunk.js.map
--- a/x/static/js/6391.aabba4a1.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/6395.f6027b24.chunk.js
--- a/x/static/js/6395.f6027b24.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/6397.8fc250af.chunk.js
--- a/x/static/js/6397.8fc250af.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/6514.d36ecbb8.chunk.js
--- a/x/static/js/6514.d36ecbb8.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/6514.d36ecbb8.chunk.js.map
--- a/x/static/js/6514.d36ecbb8.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/6526.b2c8fd93.chunk.js
--- a/x/static/js/6526.b2c8fd93.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/6621.cf64e54c.chunk.js
--- a/x/static/js/6621.cf64e54c.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/6621.cf64e54c.chunk.js.map
--- a/x/static/js/6621.cf64e54c.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/static/js/6658.fe512b5a.chunk.js
--- a/x/static/js/6658.fe512b5a.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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* as React from \'react\';\\n/**\\n * Provides information about the current step in Stepper.\\n */\\nconst StepContext = /*#__PURE__*/React.createContext({});\\nif (process.env.NODE_ENV !== \'production\') {\\n StepContext.displayName = \'StepContext\';\\n}\\n\\n/**\\n * Returns the current StepContext or an empty object if no StepContext\\n * has been defined in the component tree.\\n */\\nexport function useStepContext() {\\n return React.useContext(StepContext);\\n}\\nexport default StepContext;","\'use client\';\\n\\nimport * as React from \'react\';\\nimport PropTypes from \'prop-types\';\\nimport clsx from \'clsx\';\\nimport composeClasses from \'@mui/utils/composeClasses\';\\nimport capitalize from \\"../utils/capitalize.js\\";\\nimport { styled } from \\"../zero-styled/index.js\\";\\nimport memoTheme from \\"../utils/memoTheme.js\\";\\nimport { useDefaultProps } from \\"../DefaultPropsProvider/index.js\\";\\nimport StepperContext from 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borderLeftStyle: \'solid\',\\n borderLeftWidth: 1,\\n minHeight: 24\\n }\\n }]\\n };\\n}));\\nconst StepConnector = /*#__PURE__*/React.forwardRef(function StepConnector(inProps, ref) {\\n const props = useDefaultProps({\\n props: inProps,\\n name: \'MuiStepConnector\'\\n });\\n const {\\n className,\\n ...other\\n } = props;\\n const {\\n alternativeLabel,\\n orientation = \'horizontal\'\\n } = React.useContext(StepperContext);\\n const {\\n active,\\n disabled,\\n completed\\n } = React.useContext(StepContext);\\n const ownerState = {\\n ...props,\\n alternativeLabel,\\n orientation,\\n active,\\n completed,\\n disabled\\n };\\n const classes = useUtilityClasses(ownerState);\\n return /*#__PURE__*/_jsx(StepConnectorRoot, {\\n className: clsx(classes.root, className),\\n ref: ref,\\n ownerState: ownerState,\\n ...other,\\n children: /*#__PURE__*/_jsx(StepConnectorLine, {\\n className: classes.line,\\n ownerState: ownerState\\n })\\n });\\n});\\nprocess.env.NODE_ENV !== \\"production\\" 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--- a/x/static/js/6683.2a35f0fe.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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--- a/x/static/js/6703.faa93a20.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/6746.8d3f75be.chunk.js.map
--- a/x/static/js/6746.8d3f75be.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/6785.07d4b66b.chunk.js
--- a/x/static/js/6785.07d4b66b.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/6799.754a77ae.chunk.js
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/6823.6e35b0cf.chunk.js
--- a/x/static/js/6823.6e35b0cf.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/6823.6e35b0cf.chunk.js.map
--- a/x/static/js/6823.6e35b0cf.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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readVal !== undefined\\n : `${readVal}` !== `${filterVal}`\\n ) {\\n continue\\n }\\n }\\n\\n if (readName && record.get(\'name\') !== readName) {\\n continue\\n }\\n\\n observer.next(new BamSlightlyLazyFeature(record, this, ref))\\n }\\n observer.complete()\\n })\\n }, signal)\\n }\\n\\n async getMultiRegionFeatureDensityStats(\\n regions: Region[],\\n opts?: BaseOptions,\\n ) {\\n const { bam } = await this.configure()\\n // this is a method to avoid calling on htsget adapters\\n if (bam.index) {\\n const bytes = await bytesForRegions(regions, bam)\\n const fetchSizeLimit = this.getConf(\'fetchSizeLimit\')\\n return { bytes, fetchSizeLimit }\\n }\\n return super.getMultiRegionFeatureDensityStats(regions, opts)\\n }\\n\\n freeResources(/* { region } */): void {}\\n\\n // depends on setup being called before the BAM constructor\\n refIdToName(refId: number) {\\n return this.samHeader?.idToName[refId]\\n }\\n}\\n","import { BamFile, HtsgetFile } from \'@gmod/bam\'\\nimport { BaseFeatureDataAdapter } from \'@jbrowse/core/data_adapters/BaseAdapter\'\\nimport BamAdapter from \'../BamAdapter/BamAdapter\'\\n\\nexport default class HtsgetBamAdapter extends BamAdapter {\\n protected async configurePre() {\\n const htsgetBase = this.getConf(\'htsgetBase\')\\n const htsgetTrackId = this.getConf(\'htsgetTrackId\')\\n const bam = new HtsgetFile({\\n baseUrl: htsgetBase,\\n trackId: htsgetTrackId,\\n }) as unknown as BamFile\\n\\n const adapterConfig = this.getConf(\'sequenceAdapter\')\\n if (adapterConfig && this.getSubAdapter) {\\n const adapter = await this.getSubAdapter(adapterConfig)\\n return {\\n bam,\\n sequenceAdapter: adapter.dataAdapter as BaseFeatureDataAdapter,\\n }\\n }\\n return { bam }\\n }\\n}\\n"],"names":["BamSlightlyLazyFeature","constructor","record","adapter","ref","_get_name","this","get","_get_type","_get_score","_get_flags","flags","_get_strand","isReverseComplemented","_get_pair_orientation","isPaired","getPairOrientation","undefined","_get_next_ref","refIdToName","_next_refid","_get_next_pos","_next_pos","_get_next_segment_position","_get_seq","getReadBases","qualRaw","set","tags","properties","Object","getOwnPropertyNames","prototype","Set","filter","prop","startsWith","map","methodName","replace","concat","_tags","id","field","_get_refName","seq_id","parent","children","pairedFeature","toJSON","fromEntries","t","elt","uniqueId","_get_mismatches","getMismatches","_get_clipPos","cigar","getClip","BamAdapter","BaseFeatureDataAdapter","configurePre","bamLocation","getConf","location","indexType","pm","pluginManager","csi","bam","BamFile","bamFilehandle","openLocation","csiFilehandle","baiFilehandle","yieldThreadTime","Number","POSITIVE_INFINITY","adapterConfig","getSubAdapter","dataAdapter","sequenceAdapter","configure","configureP","catch","e","getHeader","opts","getHeaderText","setupPre","statusCallback","samHeader","updateStatus","async","idToName","nameToId","l","tag","forEach","sqLine","refId","SN","data","find","item","refName","value","setup","setupP","getRefNames","seqFetch","start","end","features","getFeatures","assemblyName","seqChunks","firstValueFrom","pipe","toArray","sequence","sort","a","b","chunk","chunkStart","chunkEnd","trimStart","Math","max","trimLength","min","chunkSeq","slice","length","Error","toLocaleString","region","originalRefName","signal","filterBy","ObservableCreate","records","getRecordsForRange","flagInclude","flagExclude","tagFilter","readName","readVal","filterVal","observer","next","complete","getMultiRegionFeatureDensityStats","regions","index","bytes","bytesForRegions","fetchSizeLimit","super","freeResources","HtsgetBamAdapter","htsgetBase","htsgetTrackId","HtsgetFile","baseUrl","trackId"],"sourceRoot":""}\n\\ No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/6833.c77c5928.chunk.js
--- a/x/static/js/6833.c77c5928.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,2 +0,0 @@
-"use strict";(globalThis.webpackChunk_jbrowse_web=globalThis.webpackChunk_jbrowse_web||[]).push([[6833],{86833:(e,t,s)=>{s.r(t),s.d(t,{default:()=>c,makeFeatures:()=>u});var a=s(46377),r=s(6434),n=s(66885),o=s(68584);function u(e){const t=new Map;for(const s of e){const e=new r.A(s),a=e.get("refName");let n=t.get(a);n||(n=[],t.set(a,n)),n.push(e)}for(const e of t.values())e.sort(((e,t)=>e.get("start")-t.get("start")));return t}class c extends a.BaseFeatureDataAdapter{constructor(e,t,s){super(e,t,s);const a=(0,o.readConfObject)(e,"features");this.features=u(a)}async getRefNames(){return[...this.features.keys()]}async getRefNameAliases(){return[...this.features.values()].map((e=>({refName:e[0].get("refName"),aliases:e[0].get("aliases")})))}getFeatures(e){const{refName:t,start:s,end:a}=e;return(0,n.ObservableCreate)((async e=>{const r=this.features.get(t)||[];for(const t of r)t.get("end")>s&&t.get("start")<a&&e.next(t);e.complete()}))}freeResources(){}}}}]);
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/6833.c77c5928.chunk.js.map
--- a/x/static/js/6833.c77c5928.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/static/js/6834.bc9e9f2b.chunk.js
--- a/x/static/js/6834.bc9e9f2b.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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-"use strict";(globalThis.webpackChunk_jbrowse_web=globalThis.webpackChunk_jbrowse_web||[]).push([[6834],{6834:(e,t,r)=>{r.r(t),r.d(t,{default:()=>d});var s=r(93902),a=r(60972),n=r(46377),i=r(99834),o=r(66885),c=r(99546),u=r(4101);class d extends n.BaseFeatureDataAdapter{async configurePre(e){const t=this.pluginManager,r=new s.C({filehandle:(0,i.openLocation)(this.getConf("bigBedLocation"),t)}),n=await r.getHeader(e);return{bigbed:r,header:n,parser:new a.A({autoSql:n.autoSql})}}async configure(e){return this.cached||(this.cached=this.configurePre(e).catch((e=>{throw this.cached=void 0,e}))),this.cached}async getRefNames(e){const{header:t}=await this.configure(e);return Object.keys(t.refsByName)}async getHeader(e){const{parser:t,header:r}=await this.configure(e),{version:s,fileType:a}=r,{fields:n,...i}=t.autoSql;return{version:s,fileType:a,autoSql:{...i},fields:Object.fromEntries(n.map((({name:e,comment:t})=>[e,t])))}}async getFeaturesHelper(e,t,r,s,a=e){const{signal:n}=t,i=this.getConf("scoreColumn"),o=this.getConf("aggregateField"),{parser:d,bigbed:f}=await this.configure(t),h=await f.getFeatures(e.refName,e.start,e.end,{signal:n,basesPerSpan:e.end-e.start});if(s&&h.length){let s=Number.POSITIVE_INFINITY,a=Number.NEGATIVE_INFINITY;for(const e of h)e.start<s&&(s=e.start),e.end>a&&(a=e.end);if(a>e.end||s<e.start)return void await this.getFeaturesHelper({...e,start:s,end:a},t,r,!1,e)}const l={};if(h.some((e=>void 0===e.uniqueId)))throw new Error("found uniqueId undefined");for(const t of h){const s=d.parseLine(`${e.refName}\t${t.start}\t${t.end}\t${t.rest}`,{uniqueId:t.uniqueId}),n=s[o];l[n]||(l[n]=[]);const{uniqueId:f,type:h,chromStart:m,chromStarts:p,blockStarts:b,blockCount:S,blockSizes:k,chromEnd:N,thickStart:g,thickEnd:y,chrom:I,score:C,...w}=s,q=S?(0,u.zZ)({chromStarts:p,blockStarts:b,blockCount:S,blockSizes:k,uniqueId:f,refName:e.refName,start:t.start}):[];if((0,u.Vl)(s)){const 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--- a/x/static/js/6837.a706c464.chunk.js Fri Oct 18 11:57:55 2024 +0000
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--- a/x/static/js/6861.66a2e4c0.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/6932.a37ea756.chunk.js
--- a/x/static/js/6932.a37ea756.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/6932.a37ea756.chunk.js.map
--- a/x/static/js/6932.a37ea756.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/6946.dd09a891.chunk.js
--- a/x/static/js/6946.dd09a891.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/6946.dd09a891.chunk.js.map
--- a/x/static/js/6946.dd09a891.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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false\\n}\\n"],"names":["fillRectCtx","x","y","width","height","ctx","fillColor","fillStyle","fillRect","strokeRectCtx","strokeColor","strokeStyle","strokeRect","getPairedColor","type","v0","v1","stats","getPairedInsertSizeAndOrientationColor","getPairedOrientationColor","getPairedInsertSizeColor","s","Math","min","start","e","max","end","log10","abs","drawFeats","self","chainData","assemblyManager","getSession","view","getContainingView","assemblyName","assemblyNames","asm","get","hasPairedReads","coords","featureHeight","getConf","colorBy","chains","chain","length","ra1","getCanonicalRefName","refName","ra2","r1s","bpToPx","coord","offsetPx","r1e","r2s","r2e","distance","undefined","push","drawSingletons","w1","maxD","log","map","c","minD","scaler","w2","fill","stroke","top","halfHeight","w","drawPairChains","distances","minXs","minX","Number","MAX_VALUE","maxX","MIN_VALUE","elt","rs","re","i","c1","primaryStrand","flags","res","SA","split","strand","ra","l","drawLongReadChains","features","f","values"],"sourceRoot":""}\n\\ 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diff -r cec274db51c0 -r ed3a21033188 x/static/js/6999.3486cca0.chunk.js
--- a/x/static/js/6999.3486cca0.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/6999.3486cca0.chunk.js.map
--- a/x/static/js/6999.3486cca0.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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(\\n <GenomicSequence feature={feature} model={model} sequence={seq} />\\n ) : mode === \'genomic_sequence_updownstream\' ? (\\n <GenomicSequence\\n model={model}\\n feature={feature}\\n sequence={seq}\\n upstream={upstream}\\n downstream={downstream}\\n />\\n ) : mode === \'cds\' ? (\\n <CDSSequence model={model} cds={cds} sequence={seq} />\\n ) : mode === \'cdna\' ? (\\n <CDNASequence\\n model={model}\\n exons={exons}\\n feature={feature}\\n cds={cds}\\n utr={utr}\\n sequence={seq}\\n />\\n ) : mode === \'protein\' ? (\\n <ProteinSequence\\n model={model}\\n cds={cds}\\n codonTable={codonTable}\\n sequence={seq}\\n />\\n ) : mode === \'gene\' ? (\\n <CDNASequence\\n model={model}\\n exons={exons}\\n feature={feature}\\n cds={cds}\\n utr={utr}\\n sequence={seq}\\n includeIntrons\\n />\\n ) : mode === \'gene_collapsed_intron\' ? 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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7013.5240d550.chunk.js
--- a/x/static/js/7013.5240d550.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7013.5240d550.chunk.js.map
--- a/x/static/js/7013.5240d550.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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b.get('start'))\n }\n\n return features\n}\n\nexport default class FromConfigAdapter extends BaseFeatureDataAdapter {\n protected features: Map<string, Feature[]>\n\n constructor(\n conf: AnyConfigurationModel,\n getSubAdapter?: getSubAdapterType,\n pluginManager?: PluginManager,\n ) {\n super(conf, getSubAdapter, pluginManager)\n const feats = readConfObject(conf, 'features') as SimpleFeatureSerialized[]\n this.features = makeFeatures(feats)\n }\n\n async getRefNames() {\n return [...this.features.keys()]\n }\n\n async getRefNameAliases() {\n return [...this.features.values()].map(featureArray => ({\n refName: featureArray[0]!.get('refName'),\n aliases: featureArray[0]!.get('aliases'),\n }))\n }\n\n getFeatures(region: NoAssemblyRegion) {\n const { refName, start, end } = region\n\n return ObservableCreate<Feature>(async observer => {\n const features = this.features.get(refName) || []\n for (const f of features) {\n if (f.get('end') > start && f.get('start') < end) {\n observer.next(f)\n }\n }\n observer.complete()\n })\n }\n\n freeResources(/* { region } */): void {}\n}\n","import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { NoAssemblyRegion } from '@jbrowse/core/util/types'\nimport { toArray } from 'rxjs/operators'\nimport { RegionsAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'\n\n// locals\nimport FromConfigAdapter from '../FromConfigAdapter/FromConfigAdapter'\nimport { firstValueFrom } from 'rxjs'\n\nexport default class FromConfigSequenceAdapter\n extends FromConfigAdapter\n implements RegionsAdapter\n{\n /**\n * Fetch features for a certain region\n * @param region - Region\n * @returns Observable of Feature objects in the region\n */\n getFeatures(region: NoAssemblyRegion) {\n return ObservableCreate<Feature>(async observer => {\n const feats = await firstValueFrom(\n super.getFeatures(region).pipe(toArray()),\n )\n const feat = feats[0]!\n observer.next(\n new SimpleFeature({\n ...feat.toJSON(),\n uniqueId: `${feat.id()}:${region.start}-${region.end}`,\n end: region.end,\n start: region.start,\n seq: feat\n .get('seq')\n .slice(\n Math.max(region.start - feat.get('start'), 0),\n Math.max(region.end - feat.get('start'), 0),\n ),\n }),\n )\n\n observer.complete()\n })\n }\n\n /**\n * Get refName, start, and end for all features after collapsing any overlaps\n */\n async getRegions() {\n const regions = []\n\n // recall: features are stored in this object sorted by start coordinate\n for (const [refName, features] of this.features) {\n let currentRegion:\n | { start: number; end: number; refName: string }\n | undefined\n for (const feature of features) {\n if (\n currentRegion &&\n currentRegion.end >= feature.get('start') &&\n currentRegion.start <= feature.get('end')\n ) {\n currentRegion.end = feature.get('end')\n } else {\n if (currentRegion) {\n regions.push(currentRegion)\n }\n currentRegion = {\n refName,\n start: feature.get('start'),\n end: feature.get('end'),\n }\n }\n }\n if (currentRegion) {\n regions.push(currentRegion)\n }\n }\n\n return regions\n }\n\n /**\n * called to provide a hint that data tied to a certain region\n * will not be needed for the foreseeable future and can be purged\n * from caches, etc\n */\n freeResources(/* { region } */): void {}\n}\n"],"names":["makeFeatures","fdata","features","Map","entry","f","SimpleFeature","refName","get","bucket","set","push","refFeatures","values","sort","a","b","FromConfigAdapter","BaseFeatureDataAdapter","constructor","conf","getSubAdapter","pluginManager","super","feats","readConfObject","this","getRefNames","keys","getRefNameAliases","map","featureArray","aliases","getFeatures","region","start","end","ObservableCreate","async","observer","next","complete","freeResources","FromConfigSequenceAdapter","feat","firstValueFrom","pipe","toArray","toJSON","uniqueId","id","seq","slice","Math","max","getRegions","regions","currentRegion","feature"],"sourceRoot":""}
\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/static/js/7067.e9508417.chunk.js
--- a/x/static/js/7067.e9508417.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7087.79101e8e.chunk.js
--- a/x/static/js/7087.79101e8e.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7117.b3239756.chunk.js
--- a/x/static/js/7117.b3239756.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7117.b3239756.chunk.js.map
--- a/x/static/js/7117.b3239756.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7126.b4b7d70b.chunk.js
--- a/x/static/js/7126.b4b7d70b.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7126.b4b7d70b.chunk.js.map
--- a/x/static/js/7126.b4b7d70b.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7181.938de865.chunk.js
--- a/x/static/js/7181.938de865.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7181.938de865.chunk.js.map
--- a/x/static/js/7181.938de865.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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--- a/x/static/js/7203.03e2b86a.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7203.03e2b86a.chunk.js.map
--- a/x/static/js/7203.03e2b86a.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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PropTypes.string,\\n /**\\n * The color of the component.\\n * It supports both default and custom theme colors, which can be added as shown in the\\n * [palette customization guide](https://mui.com/material-ui/customization/palette/#custom-colors).\\n * @default \'primary\'\\n */\\n color: PropTypes /* @typescript-to-proptypes-ignore */.oneOfType([PropTypes.oneOf([\'inherit\', \'primary\', \'secondary\', \'error\', \'info\', \'success\', \'warning\']), PropTypes.string]),\\n /**\\n * If `true`, the shrink animation is disabled.\\n * This only works if variant is `indeterminate`.\\n * @default false\\n */\\n disableShrink: chainPropTypes(PropTypes.bool, props => {\\n if (props.disableShrink && props.variant && props.variant !== \'indeterminate\') {\\n return new Error(\'MUI: You have provided the `disableShrink` prop \' + \'with a variant other than `indeterminate`. This will have no effect.\');\\n }\\n return null;\\n }),\\n /**\\n * The size of the component.\\n * If using a number, the pixel unit is assumed.\\n * If using a string, you need to provide the CSS unit, for example \'3rem\'.\\n * @default 40\\n */\\n size: PropTypes.oneOfType([PropTypes.number, PropTypes.string]),\\n /**\\n * @ignore\\n */\\n style: PropTypes.object,\\n /**\\n * The system prop that allows defining system overrides as well as additional CSS styles.\\n */\\n sx: PropTypes.oneOfType([PropTypes.arrayOf(PropTypes.oneOfType([PropTypes.func, PropTypes.object, PropTypes.bool])), PropTypes.func, PropTypes.object]),\\n /**\\n * The thickness of the circle.\\n * @default 3.6\\n */\\n thickness: PropTypes.number,\\n /**\\n * The value of the progress indicator for the determinate variant.\\n * Value between 0 and 100.\\n * @default 0\\n */\\n value: PropTypes.number,\\n /**\\n * The variant to use.\\n * Use indeterminate when there is no progress value.\\n * @default \'indeterminate\'\\n */\\n variant: PropTypes.oneOf([\'determinate\', \'indeterminate\'])\\n} : void 0;\\nexport default CircularProgress;","import generateUtilityClasses from \'@mui/utils/generateUtilityClasses\';\\nimport generateUtilityClass from \'@mui/utils/generateUtilityClass\';\\nexport function getCircularProgressUtilityClass(slot) {\\n return generateUtilityClass(\'MuiCircularProgress\', slot);\\n}\\nconst circularProgressClasses = generateUtilityClasses(\'MuiCircularProgress\', [\'root\', \'determinate\', \'indeterminate\', \'colorPrimary\', \'colorSecondary\', \'svg\', \'circle\', \'circleDeterminate\', \'circleIndeterminate\', \'circleDisableShrink\']);\\nexport default circularProgressClasses;"],"names":["circularRotateKeyframe","circularDashKeyframe","rotateAnimation","dashAnimation","CircularProgressRoot","name","slot","overridesResolver","props","styles","ownerState","root","variant","color","theme","display","variants","style","transition","transitions","create","animation","Object","entries","palette","filter","map","vars","main","CircularProgressSVG","svg","CircularProgressCircle","circle","disableShrink","circleDisableShrink","stroke","strokeDasharray","strokeDashoffset","inProps","ref","className","size","thickness","value","other","classes","slots","useUtilityClasses","circleStyle","rootStyle","rootProps","circumference","Math","PI","toFixed","round","transform","width","height","role","children","viewBox","cx","cy","r","fill","strokeWidth","getCircularProgressUtilityClass"],"sourceRoot":""}\n\\ No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/722.4329bc98.chunk.js
--- a/x/static/js/722.4329bc98.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/722.4329bc98.chunk.js.map
--- a/x/static/js/722.4329bc98.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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Toolbar.propTypes /* remove-proptypes */ = {\\n // \xe2\x94\x8c\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80 Warning \xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x90\\n // \xe2\x94\x82 These PropTypes are generated from the TypeScript type definitions. \xe2\x94\x82\\n // \xe2\x94\x82 To update them, edit the d.ts file and run `pnpm proptypes`. \xe2\x94\x82\\n // \xe2\x94\x94\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x98\\n /**\\n * The Toolbar children, usually a mixture of `IconButton`, `Button` and `Typography`.\\n * The Toolbar is a flex container, allowing flex item properties to be used to lay out the children.\\n */\\n children: PropTypes.node,\\n /**\\n * Override or extend the styles applied to the component.\\n */\\n classes: PropTypes.object,\\n /**\\n * @ignore\\n */\\n className: PropTypes.string,\\n /**\\n * The component used for the root node.\\n * Either a string to use a HTML element or a component.\\n */\\n component: PropTypes.elementType,\\n /**\\n * If `true`, disables gutter padding.\\n * @default false\\n */\\n disableGutters: PropTypes.bool,\\n /**\\n * The system prop that allows defining system overrides as well as additional CSS styles.\\n */\\n sx: PropTypes.oneOfType([PropTypes.arrayOf(PropTypes.oneOfType([PropTypes.func, PropTypes.object, PropTypes.bool])), PropTypes.func, PropTypes.object]),\\n /**\\n * The variant to use.\\n * @default \'regular\'\\n */\\n variant: PropTypes /* @typescript-to-proptypes-ignore */.oneOfType([PropTypes.oneOf([\'dense\', \'regular\']), PropTypes.string])\\n} : void 0;\\nexport default Toolbar;","import generateUtilityClasses from \'@mui/utils/generateUtilityClasses\';\\nimport generateUtilityClass from \'@mui/utils/generateUtilityClass\';\\nexport function getToolbarUtilityClass(slot) {\\n return generateUtilityClass(\'MuiToolbar\', slot);\\n}\\nconst toolbarClasses = generateUtilityClasses(\'MuiToolbar\', [\'root\', \'gutters\', \'regular\', \'dense\']);\\nexport default toolbarClasses;"],"names":["circularRotateKeyframe","circularDashKeyframe","rotateAnimation","dashAnimation","CircularProgressRoot","name","slot","overridesResolver","props","styles","ownerState","root","variant","color","theme","display","variants","style","transition","transitions","create","animation","Object","entries","palette","filter","map","vars","main","CircularProgressSVG","svg","CircularProgressCircle","circle","disableShrink","circleDisableShrink","stroke","strokeDasharray","strokeDashoffset","inProps","ref","className","size","thickness","value","other","classes","slots","useUtilityClasses","circleStyle","rootStyle","rootProps","circumference","Math","PI","toFixed","round","transform","width","height","role","children","viewBox","cx","cy","r","fill","strokeWidth","getCircularProgressUtilityClass","mapEventPropToEvent","eventProp","substring","toLowerCase","ClickAwayListener","disableReactTree","mouseEvent","onClickAway","touchEvent","movedRef","nodeRef","activatedRef","syntheticEventRef","setTimeout","current","handleRef","handleClickAway","event","insideReactTree","doc","documentElement","clientWidth","clientX","clientHeight","clientY","clickedRootScrollbar","insideDOM","composedPath","includes","contains","target","createHandleSynthetic","handlerName","childrenPropsHandler","childrenProps","mappedTouchEvent","handleTouchMove","addEventListener","removeEventListener","mappedMouseEvent","ToolbarRoot","disableGutters","gutters","position","alignItems","paddingLeft","spacing","paddingRight","breakpoints","up","minHeight","mixins","toolbar","component","as","getToolbarUtilityClass"],"sourceRoot":""}\n\\ No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/7309.f9d18abb.chunk.js
--- a/x/static/js/7309.f9d18abb.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7309.f9d18abb.chunk.js.map
--- a/x/static/js/7309.f9d18abb.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
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\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/static/js/7348.40afbdc0.chunk.js
--- a/x/static/js/7348.40afbdc0.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7348.40afbdc0.chunk.js.map
--- a/x/static/js/7348.40afbdc0.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7374.932d083d.chunk.js
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7374.932d083d.chunk.js.map
--- a/x/static/js/7374.932d083d.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7389.fa6a1eb0.chunk.js
--- a/x/static/js/7389.fa6a1eb0.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7389.fa6a1eb0.chunk.js.map
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React from 'react'\nimport { Paper, Typography } from '@mui/material'\nimport { makeStyles } from 'tss-react/mui'\n\n// icons\nimport ErrorIcon from '@mui/icons-material/Error'\n\nconst useStyles = makeStyles()(theme => ({\n error: {\n margin: theme.spacing(2),\n },\n errorHeader: {\n background: theme.palette.error.light,\n color: theme.palette.error.contrastText,\n padding: theme.spacing(2),\n textAlign: 'center',\n },\n errorMessage: {\n padding: theme.spacing(2),\n },\n}))\n\nexport default function ImportError({ error }: { error: unknown }) {\n const { classes } = useStyles()\n return (\n <Paper className={classes.error}>\n <div className={classes.errorHeader}>\n <ErrorIcon color=\"inherit\" fontSize=\"large\" />\n <div>\n <Typography variant=\"h6\" color=\"inherit\" align=\"center\">\n Import error\n </Typography>\n </div>\n </div>\n <Typography className={classes.errorMessage}>{`${error}`}</Typography>\n </Paper>\n )\n}\n","import React, { useState } from 'react'\nimport { IAnyStateTreeNode } from 'mobx-state-tree'\nimport { Button, Paper, Typography, alpha } from '@mui/material'\nimport { getSession } from '@jbrowse/core/util'\nimport { makeStyles } from 'tss-react/mui'\nimport { observer } from 'mobx-react'\nimport { useDropzone } from 'react-dropzone'\n\n// icons\nimport CloudUploadIcon from '@mui/icons-material/CloudUpload'\n\n// locals\nimport ImportError from './ImportError'\n\nconst MAX_FILE_SIZE = 512 * 1024 ** 2 // 512 MiB\n\nfunction styledBy(property: string, mapping: Record<string, string>) {\n return (props: Record<string, string>) => mapping[props[property]!]\n}\n\n// @ts-expect-error\nconst useStyles = makeStyles()(theme => ({\n root: {\n margin: theme.spacing(1),\n },\n paper: {\n display: 'flex',\n flexDirection: 'column',\n },\n dropZone: {\n textAlign: 'center',\n margin: theme.spacing(2),\n padding: theme.spacing(2),\n borderWidth: 2,\n borderRadius: 2,\n borderColor: styledBy('isDragActive', {\n true: theme.palette.secondary.light,\n false: theme.palette.divider,\n }),\n borderStyle: 'dashed',\n backgroundColor: styledBy('isDragActive', {\n true: alpha(\n theme.palette.text.primary,\n theme.palette.action.hoverOpacity,\n ),\n false: theme.palette.background.default,\n }),\n outline: 'none',\n transition: 'border .24s ease-in-out',\n '&:focus': {\n borderColor: theme.palette.secondary.light,\n },\n },\n uploadIcon: {\n color: theme.palette.text.secondary,\n },\n}))\n\nconst ImportSessionWidget = observer(function ({\n model,\n}: {\n model: IAnyStateTreeNode\n}) {\n const [error, setError] = useState<unknown>()\n const { getRootProps, getInputProps, isDragActive } = useDropzone({\n // @ts-expect-error\n accept: 'application/json',\n maxSize: MAX_FILE_SIZE,\n multiple: false,\n onDrop: async (acceptedFiles, rejectedFiles) => {\n try {\n if (rejectedFiles.length > 0) {\n throw new Error(rejectedFiles[0]!.errors.map(e => `${e}`).join(', '))\n }\n const sessionText = await acceptedFiles[0]!.text()\n 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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7407.4421929d.chunk.js
--- a/x/static/js/7407.4421929d.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7407.4421929d.chunk.js.map
--- a/x/static/js/7407.4421929d.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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SpeedDialAction.propTypes /* remove-proptypes */ = {\\n // \xe2\x94\x8c\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80 Warning \xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x90\\n // \xe2\x94\x82 These PropTypes are generated from the TypeScript type definitions. \xe2\x94\x82\\n // \xe2\x94\x82 To update them, edit the d.ts file and run `pnpm proptypes`. 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*/\\n className: PropTypes.string,\\n /**\\n * Adds a transition delay, to allow a series of SpeedDialActions to be animated.\\n * @default 0\\n */\\n delay: PropTypes.number,\\n /**\\n * Props applied to the [`Fab`](https://mui.com/material-ui/api/fab/) component.\\n * @default {}\\n */\\n FabProps: PropTypes.object,\\n /**\\n * The icon to display in the SpeedDial Fab.\\n */\\n icon: PropTypes.node,\\n /**\\n * This prop is used to help implement the accessibility logic.\\n * If you don\'t provide this prop. It falls back to a randomly generated id.\\n */\\n id: PropTypes.string,\\n /**\\n * If `true`, the component is shown.\\n */\\n open: PropTypes.bool,\\n /**\\n * The system prop that allows defining system overrides as well as additional CSS styles.\\n */\\n sx: PropTypes.oneOfType([PropTypes.arrayOf(PropTypes.oneOfType([PropTypes.func, PropTypes.object, PropTypes.bool])), PropTypes.func, PropTypes.object]),\\n /**\\n * `classes` prop applied to the [`Tooltip`](https://mui.com/material-ui/api/tooltip/) element.\\n */\\n TooltipClasses: PropTypes.object,\\n /**\\n * Make the tooltip always visible when the SpeedDial is open.\\n * @default false\\n */\\n tooltipOpen: PropTypes.bool,\\n /**\\n * Placement of the tooltip.\\n * @default \'left\'\\n */\\n tooltipPlacement: PropTypes.oneOf([\'bottom-end\', \'bottom-start\', \'bottom\', \'left-end\', \'left-start\', \'left\', \'right-end\', \'right-start\', \'right\', \'top-end\', \'top-start\', \'top\']),\\n /**\\n * Label to display in the tooltip.\\n */\\n tooltipTitle: PropTypes.node\\n} : void 0;\\nexport default SpeedDialAction;"],"names":["FabRoot","name","slot","shouldForwardProp","prop","overridesResolver","props","styles","ownerState","root","variant","size","color","colorInherit","theme","typography","button","minHeight","transition","transitions","create","duration","short","borderRadius","padding","minWidth","width","height","zIndex","vars","fab","boxShadow","shadows","palette","text","primary","getContrastText","grey","backgroundColor","A100","textDecoration","focusVisible","variants","style","Object","entries","filter","map","contrastText","main","dark","disabled","action","disabledBackground","inProps","ref","children","className","component","disableFocusRipple","focusVisibleClassName","other","classes","slots","composedClasses","useUtilityClasses","focusRipple","getFabUtilityClass","getSpeedDialActionUtilityClass","generateUtilityClass","generateUtilityClasses","SpeedDialActionFab","styled","Fab","skipVariantsResolver","open","fabClosed","memoTheme","margin","secondary","background","paper","SpeedDialAction","fabHoverBg","shorter","opacity","transform","SpeedDialActionStaticTooltip","staticTooltip","staticTooltipClosed","capitalize","tooltipPlacement","position","display","alignItems","staticTooltipLabel","transformOrigin","right","marginRight","left","marginLeft","SpeedDialActionStaticTooltipLabel","body1","shape","wordBreak","delay","FabProps","icon","id","TooltipClasses","tooltipOpen","tooltipOpenProp","tooltipTitle","composeClasses","setTooltipOpen","transitionStyle","transitionDelay","clsx","tabIndex","role","Tooltip","title","placement","onClose","onOpen"],"sourceRoot":""}\n\\ No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/7409.8e71acc1.chunk.js
--- a/x/static/js/7409.8e71acc1.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7409.8e71acc1.chunk.js.map
--- a/x/static/js/7409.8e71acc1.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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end: number },\\n line: string,\\n fileOffset: number,\\n ) {\\n const fields = line.split(\'\\\\t\')\\n\\n // note: index column numbers are 1-based\\n return {\\n start: +fields[columnNumbers.start - 1]!,\\n end: +fields[columnNumbers.end - 1]!,\\n lineHash: fileOffset,\\n fields,\\n }\\n }\\n\\n public freeResources(/* { region } */) {}\\n}\\n","import { GFF3FeatureLineWithRefs } from \'gff-nostream\'\\n\\ninterface GFF3Feature {\\n start: number\\n end: number\\n strand?: number\\n type: string | null\\n source: string | null\\n refName: string\\n derived_features: unknown[] | null\\n phase?: number\\n score?: number\\n subfeatures: GFF3Feature[] | undefined\\n [key: string]: unknown\\n}\\n\\nexport function featureData(data: GFF3FeatureLineWithRefs): GFF3Feature {\\n const {\\n end,\\n start,\\n child_features,\\n derived_features,\\n attributes,\\n type,\\n source,\\n phase,\\n seq_id,\\n score,\\n strand,\\n } = data\\n\\n let strand2: number | undefined\\n if (strand === \'+\') {\\n strand2 = 1\\n } else if (strand === \'-\') {\\n strand2 = -1\\n } else if (strand === \'.\') {\\n strand2 = 0\\n }\\n\\n const defaultFields = new Set([\\n \'start\',\\n \'end\',\\n \'seq_id\',\\n \'score\',\\n \'type\',\\n \'source\',\\n \'phase\',\\n \'strand\',\\n ])\\n const dataAttributes = attributes || {}\\n const resultAttributes = {} as Record<string, unknown>\\n for (const a of Object.keys(dataAttributes)) {\\n let b = a.toLowerCase()\\n if (defaultFields.has(b)) {\\n // add \\"suffix\\" to tag name if it already exists\\n // reproduces behavior of NCList\\n b += \'2\'\\n }\\n if (dataAttributes[a] && a !== \'_lineHash\') {\\n let attr: string | string[] | undefined = dataAttributes[a]\\n if (Array.isArray(attr) && attr.length === 1) {\\n ;[attr] = attr\\n }\\n resultAttributes[b] = attr\\n }\\n }\\n\\n return {\\n ...resultAttributes,\\n start: start! - 1,\\n end: end!,\\n strand: strand2,\\n type,\\n source,\\n refName: seq_id!,\\n derived_features,\\n phase: phase === null ? undefined : Number(phase),\\n score: score === null ? undefined : score,\\n subfeatures: child_features.flatMap(childLocs =>\\n childLocs.map(childLoc => featureData(childLoc)),\\n ),\\n }\\n}\\n"],"names":["Gff3TabixAdapter","BaseFeatureDataAdapter","constructor","config","getSubAdapter","pluginManager","super","gffGzLocation","readConfObject","indexType","location","dontRedispatch","this","gff","TabixIndexedFile","filehandle","openLocation","csiFilehandle","undefined","tbiFilehandle","chunkCacheSize","renameRefSeqs","n","getRefNames","opts","getReferenceSequenceNames","getHeader","getFeatures","query","ObservableCreate","async","metadata","getMetadata","getFeaturesHelper","observer","signal","allowRedispatch","originalQuery","lines","getLines","refName","start","end","line","fileOffset","push","parseLine","columnNumbers","length","minStart","Number","POSITIVE_INFINITY","maxEnd","NEGATIVE_INFINITY","featureType","fields","includes","gff3","map","lineRecord","lineHash","join","featureLocs","parseStringSync","featureLoc","f","SimpleFeature","data","featureData","id","attributes","_lineHash","doesIntersect2","get","next","complete","e","error","split","freeResources","child_features","derived_features","type","source","phase","seq_id","score","strand","strand2","defaultFields","Set","dataAttributes","resultAttributes","a","Object","keys","b","toLowerCase","has","attr","Array","isArray","subfeatures","flatMap","childLocs","childLoc"],"sourceRoot":""}\n\\ No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/741.a9772d36.chunk.js
--- a/x/static/js/741.a9772d36.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/741.a9772d36.chunk.js.map
--- a/x/static/js/741.a9772d36.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/static/js/7418.2ac24978.chunk.js
--- a/x/static/js/7418.2ac24978.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7418.2ac24978.chunk.js.map
--- a/x/static/js/7418.2ac24978.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7428.1e6f676f.chunk.js
--- a/x/static/js/7428.1e6f676f.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7428.1e6f676f.chunk.js.map
--- a/x/static/js/7428.1e6f676f.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7489.b8a76d29.chunk.js
--- a/x/static/js/7489.b8a76d29.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7489.b8a76d29.chunk.js.map
--- a/x/static/js/7489.b8a76d29.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7564.3a461e67.chunk.js
--- a/x/static/js/7564.3a461e67.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7564.3a461e67.chunk.js.map
--- a/x/static/js/7564.3a461e67.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7579.1b98701c.chunk.js
--- a/x/static/js/7579.1b98701c.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7579.1b98701c.chunk.js.map
--- a/x/static/js/7579.1b98701c.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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--- a/x/static/js/7584.a162e3d6.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7627.31dfd44e.chunk.js
--- a/x/static/js/7627.31dfd44e.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7627.31dfd44e.chunk.js.map
--- a/x/static/js/7627.31dfd44e.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/765.20669bca.chunk.js
--- a/x/static/js/765.20669bca.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/765.20669bca.chunk.js.map
--- a/x/static/js/765.20669bca.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
-{"version":3,"file":"static/js/765.20669bca.chunk.js","mappings":"0NAUA,MAyDA,EAzD4BA,EAC1BC,kBACAC,UACAC,gBAMA,MAAOC,EAAOC,IAAYC,EAAAA,EAAAA,YAC1B,OACEC,EAAAA,cAACC,EAAAA,OAAM,CACLC,MAAI,EACJP,QAASA,KACPA,GAAQ,EAAM,EAEhBQ,MAAO,mBAAmBT,OAE1BM,EAAAA,cAACI,EAAAA,EAAa,KACXP,EAAQG,EAAAA,cAACK,EAAAA,aAAY,CAACR,MAAOA,IAAY,KAC1CG,EAAAA,cAACM,EAAAA,EAAiB,KAAC,iCAErBN,EAAAA,cAACO,EAAAA,EAAa,KACZP,EAAAA,cAACQ,EAAAA,EAAM,CACLC,QAASA,KACPd,GAAQ,EAAM,EAEhBe,MAAM,WACP,UAGDV,EAAAA,cAACQ,EAAAA,EAAM,CACLC,QAASA,KAEN,WACC,IACMf,GACFE,EAAUe,mBAAmB,CAAEC,KAAMlB,IAEvCC,GAAQ,EACV,CAAE,MAAOkB,GACPC,QAAQjB,MAAMgB,GACdf,EAASe,EACX,CACD,EAVA,EAUG,EAENH,MAAM,UACNK,QAAQ,YACRC,WAAS,GACV,WAII,C","sources":["components/DeleteSessionDialog.tsx"],"sourcesContent":["import React, { useState } from 'react'\nimport {\n Button,\n DialogActions,\n DialogContent,\n DialogContentText,\n} from '@mui/material'\nimport { Dialog, ErrorMessage } from '@jbrowse/core/ui'\nimport type { WebRootModel } from '../rootModel/rootModel'\n\nconst DeleteSessionDialog = ({\n sessionToDelete,\n onClose,\n rootModel,\n}: {\n sessionToDelete?: string\n onClose: (_arg0: boolean) => void\n rootModel: WebRootModel\n}) => {\n const [error, setError] = useState<unknown>()\n return (\n <Dialog\n open\n onClose={() => {\n onClose(false)\n }}\n title={`Delete session \"${sessionToDelete}\"?`}\n >\n <DialogContent>\n {error ? <ErrorMessage error={error} /> : null}\n <DialogContentText>This action cannot be undone</DialogContentText>\n </DialogContent>\n <DialogActions>\n <Button\n onClick={() => {\n onClose(false)\n }}\n color=\"primary\"\n >\n Cancel\n </Button>\n <Button\n onClick={() => {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n ;(async () => {\n try {\n if (sessionToDelete) {\n rootModel.removeSavedSession({ name: sessionToDelete })\n }\n onClose(true)\n } catch (e) {\n console.error(e)\n setError(e)\n }\n })()\n }}\n color=\"primary\"\n variant=\"contained\"\n autoFocus\n >\n Delete\n </Button>\n </DialogActions>\n </Dialog>\n )\n}\n\nexport default DeleteSessionDialog\n"],"names":["DeleteSessionDialog","sessionToDelete","onClose","rootModel","error","setError","useState","React","Dialog","open","title","DialogContent","ErrorMessage","DialogContentText","DialogActions","Button","onClick","color","removeSavedSession","name","e","console","variant","autoFocus"],"sourceRoot":""}
\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/static/js/7663.e79b053a.chunk.js
--- a/x/static/js/7663.e79b053a.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7663.e79b053a.chunk.js.map
--- a/x/static/js/7663.e79b053a.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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client\\";\\n\\nimport createSvgIcon from \'./utils/createSvgIcon\';\\nimport { jsx as _jsx } from \\"react/jsx-runtime\\";\\nexport default createSvgIcon( /*#__PURE__*/_jsx(\\"path\\", {\\n d: \\"M21 7h-2v2h-2V7h-2V5h2V3h2v2h2zm-2 14-7-3-7 3V5c0-1.1.9-2 2-2h7c-.63.84-1 1.87-1 3 0 2.76 2.24 5 5 5 .34 0 .68-.03 1-.1z\\"\\n}), \'BookmarkAdd\');","import React, { useState, useEffect, lazy } from \'react\'\\nimport { getSnapshot } from \'mobx-state-tree\'\\nimport { observer } from \'mobx-react\'\\nimport { Dialog, ErrorMessage } from \'@jbrowse/core/ui\'\\nimport {\\n Button,\\n DialogActions,\\n DialogContent,\\n DialogContentText,\\n IconButton,\\n TextField,\\n Typography,\\n} from \'@mui/material\'\\nimport copy from \'copy-to-clipboard\'\\nimport { StringParam, useQueryParam } from \'use-query-params\'\\nimport { AbstractSessionModel } from \'@jbrowse/core/util\'\\n\\n// icons\\nimport SettingsIcon from \'@mui/icons-material/Settings\'\\nimport { ContentCopy as ContentCopyIcon } from \'@jbrowse/core/ui/Icons\'\\nimport BookmarkAddIcon from \'@mui/icons-material/BookmarkAdd\'\\n\\n// locals\\nimport { toUrlSafeB64 } from \'../util\'\\nimport { shareSessionToDynamo } from \'../sessionSharing\'\\n\\nconst SettingsDialog = lazy(() => import(\'./ShareSettingsDialog\'))\\n\\nconst SHARE_URL'..b' setPasswordParam(result.password)\\n } else {\\n const sess = await toUrlSafeB64(JSON.stringify(getSnapshot(session)))\\n const longUrl = new URL(window.location.href)\\n const longParams = new URLSearchParams(longUrl.search)\\n longParams.set(\'session\', `encoded-${sess}`)\\n setSessionParam(`encoded-${sess}`)\\n longUrl.search = longParams.toString()\\n setLongUrl(longUrl.toString())\\n }\\n } catch (e) {\\n setError(e)\\n } finally {\\n setLoading(false)\\n }\\n })()\\n }, [currentSetting, error, session, url, snap])\\n\\n const disabled = (currentSetting === \'short\' && loading) || !!error\\n return (\\n <>\\n <Dialog\\n maxWidth=\\"xl\\"\\n open\\n onClose={handleClose}\\n title=\\"JBrowse Shareable Link\\"\\n >\\n <DialogContent>\\n <DialogContentText>\\n Copy the URL below to share your current JBrowse session.\\n <IconButton\\n onClick={() => {\\n setSettingsDialogOpen(true)\\n }}\\n >\\n <SettingsIcon />\\n </IconButton>\\n </DialogContentText>\\n\\n {currentSetting === \'short\' ? (\\n error ? (\\n <ErrorMessage\\n error={error}\\n onReset={() => {\\n setError(undefined)\\n }}\\n />\\n ) : loading ? (\\n <Typography>Generating short URL...</Typography>\\n ) : (\\n <LinkField url={shortUrl} />\\n )\\n ) : (\\n <LinkField url={longUrl} />\\n )}\\n </DialogContent>\\n <DialogActions>\\n <Button\\n startIcon={<BookmarkAddIcon />}\\n disabled={disabled}\\n onClick={event => {\\n event.preventDefault()\\n setPassword(passwordParam, \'replaceIn\')\\n setSession(sessionParam, \'replaceIn\')\\n alert(\'Now press Ctrl+D (PC) or Cmd+D (Mac)\')\\n }}\\n >\\n Create browser Bookmark\\n </Button>\\n\\n <Button\\n onClick={() => {\\n copy(shortUrl || longUrl)\\n session.notify(\'Copied to clipboard\', \'success\')\\n }}\\n startIcon={<ContentCopyIcon />}\\n disabled={disabled}\\n >\\n Copy to Clipboard\\n </Button>\\n\\n <Button onClick={handleClose} autoFocus>\\n Close\\n </Button>\\n </DialogActions>\\n </Dialog>\\n\\n <SettingsDialog\\n open={settingsDialogOpen}\\n onClose={() => {\\n setSettingsDialogOpen(false)\\n }}\\n currentSetting={currentSetting}\\n />\\n </>\\n )\\n})\\n\\nexport default ShareDialog\\n"],"names":["createSvgIcon","d","SettingsDialog","lazy","LinkField","url","React","TextField","label","value","InputProps","readOnly","variant","fullWidth","onClick","event","target","select","observer","handleClose","session","sessionParam","setSessionParam","useState","passwordParam","setPasswordParam","shortUrl","setShortUrl","longUrl","setLongUrl","loading","setLoading","error","setError","settingsDialogOpen","setSettingsDialogOpen","setPassword","useQueryParam","StringParam","setSession","shareURL","currentSetting","localStorage","getItem","snap","getSnapshot","useEffect","locationUrl","URL","window","location","href","result","shareSessionToDynamo","params","URLSearchParams","search","set","json","sessionId","password","toString","sess","toUrlSafeB64","JSON","stringify","longParams","e","disabled","Dialog","maxWidth","open","onClose","title","DialogContent","DialogContentText","IconButton","SettingsIcon","ErrorMessage","onReset","undefined","Typography","DialogActions","Button","startIcon","BookmarkAddIcon","preventDefault","alert","copy","notify","ContentCopyIcon","autoFocus"],"sourceRoot":""}\n\\ No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/7706.430ce07e.chunk.js
--- a/x/static/js/7706.430ce07e.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7706.430ce07e.chunk.js.map
--- a/x/static/js/7706.430ce07e.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/772.83c2d2db.chunk.js
--- a/x/static/js/772.83c2d2db.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/772.83c2d2db.chunk.js.map
--- a/x/static/js/772.83c2d2db.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7753.87963fd9.chunk.js
--- a/x/static/js/7753.87963fd9.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7753.87963fd9.chunk.js.map
--- a/x/static/js/7753.87963fd9.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7761.0cf7cf29.chunk.js
--- a/x/static/js/7761.0cf7cf29.chunk.js Fri Oct 18 11:57:55 2024 +0000
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--- a/x/static/js/7761.0cf7cf29.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7773.7e072552.chunk.js
--- a/x/static/js/7773.7e072552.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7790.3790bece.chunk.js
--- a/x/static/js/7790.3790bece.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7790.3790bece.chunk.js.map
--- a/x/static/js/7790.3790bece.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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This will have no effect.\');\\n }\\n return null;\\n }),\\n /**\\n * The size of the component.\\n * If using a number, the pixel unit is assumed.\\n * If using a string, you need to provide the CSS unit, for example \'3rem\'.\\n * @default 40\\n */\\n size: PropTypes.oneOfType([PropTypes.number, PropTypes.string]),\\n /**\\n * @ignore\\n */\\n style: PropTypes.object,\\n /**\\n * The system prop that allows defining system overrides as well as additional CSS styles.\\n */\\n sx: PropTypes.oneOfType([PropTypes.arrayOf(PropTypes.oneOfType([PropTypes.func, PropTypes.object, PropTypes.bool])), PropTypes.func, PropTypes.object]),\\n /**\\n * The thickness of the circle.\\n * @default 3.6\\n */\\n thickness: PropTypes.number,\\n /**\\n * The value of the progress indicator for the determinate variant.\\n * Value between 0 and 100.\\n * @default 0\\n */\\n value: PropTypes.number,\\n /**\\n * The variant to use.\\n * Use indeterminate when there is no progress value.\\n * @default \'indeterminate\'\\n */\\n variant: PropTypes.oneOf([\'determinate\', \'indeterminate\'])\\n} : void 0;\\nexport default CircularProgress;","import generateUtilityClasses from \'@mui/utils/generateUtilityClasses\';\\nimport generateUtilityClass from \'@mui/utils/generateUtilityClass\';\\nexport function getCircularProgressUtilityClass(slot) {\\n return generateUtilityClass(\'MuiCircularProgress\', slot);\\n}\\nconst circularProgressClasses = generateUtilityClasses(\'MuiCircularProgress\', [\'root\', \'determinate\', \'indeterminate\', \'colorPrimary\', \'colorSecondary\', \'svg\', \'circle\', \'circleDeterminate\', \'circleIndeterminate\', \'circleDisableShrink\']);\\nexport default circularProgressClasses;"],"names":["LoadingMessage","React","CircularProgress","size","style","marginRight","Typography","display","TextField2","children","rest","TextField","useSvgLocal","key","val","useLocalStorage","ExportSvgDialog","model","handleClose","session","getSession","offscreenCanvas","OffscreenCanvas","rasterizeLayers","setRasterizeLayers","useState","loading","setLoading","error","setError","filename","setFilename","trackLabels","setTrackLabels","themeName","setThemeName","Dialog","open","onClose","title","DialogContent","ErrorMessage","helperText","value","onChange","event","target","select","label","variant","width","MenuItem","allThemes","Object","entries","map","name","FormControlLabel","control","Checkbox","checked","DialogActions","Button","color","onClick","type","async","undefined","exportSvg","e","console","circularRotateKeyframe","circularDashKeyframe","rotateAnimation","dashAnimation","CircularProgressRoot","slot","overridesResolver","props","styles","ownerState","root","theme","variants","transition","transitions","create","animation","palette","filter","vars","main","CircularProgressSVG","svg","CircularProgressCircle","circle","disableShrink","circleDisableShrink","stroke","strokeDasharray","strokeDashoffset","inProps","ref","className","thickness","other","classes","slots","useUtilityClasses","circleStyle","rootStyle","rootProps","circumference","Math","PI","toFixed","round","transform","height","role","viewBox","cx","cy","r","fill","strokeWidth","getCircularProgressUtilityClass"],"sourceRoot":""}\n\\ No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/7809.eb2c5f08.chunk.js
--- a/x/static/js/7809.eb2c5f08.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,2 +0,0 @@
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7809.eb2c5f08.chunk.js.map
--- a/x/static/js/7809.eb2c5f08.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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{\\n BaseFeatureDataAdapter,\\n BaseOptions,\\n} from \'@jbrowse/core/data_adapters/BaseAdapter\'\\nimport { NoAssemblyRegion } from \'@jbrowse/core/util/types\'\\nimport { openLocation } from \'@jbrowse/core/util/io\'\\nimport { ObservableCreate } from \'@jbrowse/core/util/rxjs\'\\nimport IntervalTree from \'@flatten-js/interval-tree\'\\nimport SimpleFeature, { Feature } from \'@jbrowse/core/util/simpleFeature\'\\nimport { unzip } from \'@gmod/bgzf-filehandle\'\\nimport { parseStringSync } from \'gff-nostream\'\\nimport { isGzip, updateStatus } from \'@jbrowse/core/util\'\\nimport type { Buffer } from \'buffer\'\\n\\nimport { featureData } from \'../featureData\'\\n\\ntype StatusCallback = (arg: string) => void\\n\\nexport default class Gff3Adapter extends BaseFeatureDataAdapter {\\n calculatedIntervalTreeMap: Record<string, IntervalTree> = {}\\n\\n gffFeatures?: Promise<{\\n header: string\\n intervalTree'..b'es\\n }\\n\\n public async getRefNames(opts: BaseOptions = {}) {\\n const { 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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7812.6bb31bfb.chunk.js
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7831.cfcb0221.chunk.js.map
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7842.cbff451c.chunk.js.map
--- a/x/static/js/7842.cbff451c.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/7864.59d0de32.chunk.js
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flex item properties to be used to lay out the children.\\n */\\n children: PropTypes.node,\\n /**\\n * Override or extend the styles applied to the component.\\n */\\n classes: PropTypes.object,\\n /**\\n * @ignore\\n */\\n className: PropTypes.string,\\n /**\\n * The component used for the root node.\\n * Either a string to use a HTML element or a component.\\n */\\n component: PropTypes.elementType,\\n /**\\n * If `true`, disables gutter padding.\\n * @default false\\n */\\n disableGutters: PropTypes.bool,\\n /**\\n * The system prop that allows defining system overrides as well as additional CSS styles.\\n */\\n sx: PropTypes.oneOfType([PropTypes.arrayOf(PropTypes.oneOfType([PropTypes.func, PropTypes.object, PropTypes.bool])), PropTypes.func, PropTypes.object]),\\n /**\\n * The variant to use.\\n * @default \'regular\'\\n */\\n variant: PropTypes /* @typescript-to-proptypes-ignore */.oneOfType([PropTypes.oneOf([\'dense\', \'regular\']), PropTypes.string])\\n} : void 0;\\nexport 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Is passed to child components.\\n */\\n active: PropTypes.bool,\\n /**\\n * Should be `Step` sub-components such as `StepLabel`, `StepContent`.\\n */\\n children: PropTypes.node,\\n /**\\n * Override or extend the styles applied to the component.\\n */\\n classes: PropTypes.object,\\n /**\\n * @ignore\\n */\\n className: PropTypes.string,\\n /**\\n * Mark the step as completed. Is passed to child components.\\n */\\n completed: PropTypes.bool,\\n /**\\n * The component used for the root node.\\n * Either a string to use a HTML element or a component.\\n */\\n component: PropTypes.elementType,\\n /**\\n * If `true`, the step is disabled, will also disable the button if\\n * `StepButton` is a child of `Step`. Is passed to child components.\\n */\\n disabled: PropTypes.bool,\\n /**\\n * Expand the step.\\n * @default false\\n */\\n expanded: PropTypes.bool,\\n /**\\n * The position of the step.\\n * The prop defaults to the value inherited from the parent Stepper component.\\n */\\n index: integerPropType,\\n /**\\n * If `true`, the Step is displayed as rendered last.\\n * The prop defaults to the value inherited from the parent Stepper component.\\n */\\n last: PropTypes.bool,\\n /**\\n * The system prop that allows defining system overrides as well as additional CSS styles.\\n */\\n sx: PropTypes.oneOfType([PropTypes.arrayOf(PropTypes.oneOfType([PropTypes.func, PropTypes.object, PropTypes.bool])), PropTypes.func, PropTypes.object])\\n} : void 0;\\nexport default Step;","import * as React from \'react\';\\n/**\\n * Provides information about the current step in Stepper.\\n */\\nconst StepContext = /*#__PURE__*/React.createContext({});\\nif (process.env.NODE_ENV !== \'production\') {\\n StepContext.displayName = \'StepContext\';\\n}\\n\\n/**\\n * Returns the current StepContext or an empty object if no StepContext\\n * has been defined in the component tree.\\n */\\nexport function useStepContext() {\\n return React.useContext(StepContext);\\n}\\nexport default StepContext;","import generateUtilityClasses from \'@mui/utils/generateUtilityClasses\';\\nimport generateUtilityClass from \'@mui/utils/generateUtilityClass\';\\nexport function getStepUtilityClass(slot) {\\n return generateUtilityClass(\'MuiStep\', slot);\\n}\\nconst stepClasses = generateUtilityClasses(\'MuiStep\', [\'root\', \'horizontal\', \'vertical\', \'alternativeLabel\', \'completed\']);\\nexport default stepClasses;","import * as React from \'react\';\\n/**\\n * Provides information about the current step in Stepper.\\n */\\nconst StepperContext = /*#__PURE__*/React.createContext({});\\nif (process.env.NODE_ENV !== \'production\') {\\n StepperContext.displayName = \'StepperContext\';\\n}\\n\\n/**\\n * Returns the current StepperContext or an empty object if no StepperContext\\n * has been defined in the component tree.\\n */\\nexport function useStepperContext() {\\n return React.useContext(StepperContext);\\n}\\nexport default StepperContext;"],"names":["StepRoot","name","slot","overridesResolver","props","styles","ownerState","root","orientation","alternativeLabel","completed","variants","style","paddingLeft","paddingRight","flex","position","inProps","ref","active","activeProp","children","className","component","completedProp","disabled","disabledProp","expanded","index","last","other","activeStep","connector","nonLinear","undefined","contextValue","icon","classes","slots","useUtilityClasses","newChildren","as","Provider","value","StepContext","useStepContext","getStepUtilityClass","StepperContext","useStepperContext"],"sourceRoot":""}\n\\ No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/8007.3025c802.chunk.js
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8007.3025c802.chunk.js.LICENSE.txt
--- a/x/static/js/8007.3025c802.chunk.js.LICENSE.txt Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,14 +0,0 @@
-/*! *****************************************************************************
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-Permission to use, copy, modify, and/or distribute this software for any
-purpose with or without fee is hereby granted.
-
-THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH
-REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY
-AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
-INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM
-LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR
-OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
-PERFORMANCE OF THIS SOFTWARE.
-***************************************************************************** */

diff -r cec274db51c0 -r ed3a21033188 x/static/js/8007.3025c802.chunk.js.map
--- a/x/static/js/8007.3025c802.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8052.7d772984.chunk.js
--- a/x/static/js/8052.7d772984.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8076.fc478e91.chunk.js
--- a/x/static/js/8076.fc478e91.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8076.fc478e91.chunk.js.map
--- a/x/static/js/8076.fc478e91.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8105.4fd35586.chunk.js
--- a/x/static/js/8105.4fd35586.chunk.js Fri Oct 18 11:57:55 2024 +0000
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--- a/x/static/js/8105.4fd35586.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8109.344e1845.chunk.js
--- a/x/static/js/8109.344e1845.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8120.85042513.chunk.js.map
--- a/x/static/js/8120.85042513.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8150.09c54606.chunk.js
--- a/x/static/js/8150.09c54606.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8165.d07843b4.chunk.js
--- a/x/static/js/8165.d07843b4.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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--- a/x/static/js/8187.383aefbf.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8187.383aefbf.chunk.js.map
--- a/x/static/js/8187.383aefbf.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8341.fa84fa67.chunk.js
--- a/x/static/js/8341.fa84fa67.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8341.fa84fa67.chunk.js.map
--- a/x/static/js/8341.fa84fa67.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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Toolbar.propTypes /* remove-proptypes */ = {\\n // \xe2\x94\x8c\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80 Warning \xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x90\\n // \xe2\x94\x82 These PropTypes are generated from the TypeScript type definitions. \xe2\x94\x82\\n // \xe2\x94\x82 To update them, edit the d.ts file and run `pnpm proptypes`. \xe2\x94\x82\\n 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flex item properties to be used to lay out the children.\\n */\\n children: PropTypes.node,\\n /**\\n * Override or extend the styles applied to the component.\\n */\\n classes: PropTypes.object,\\n /**\\n * @ignore\\n */\\n className: PropTypes.string,\\n /**\\n * The component used for the root node.\\n * Either a string to use a HTML element or a component.\\n */\\n component: PropTypes.elementType,\\n /**\\n * If `true`, disables gutter padding.\\n * @default false\\n */\\n disableGutters: PropTypes.bool,\\n /**\\n * The system prop that allows defining system overrides as well as additional CSS styles.\\n */\\n sx: PropTypes.oneOfType([PropTypes.arrayOf(PropTypes.oneOfType([PropTypes.func, PropTypes.object, PropTypes.bool])), PropTypes.func, PropTypes.object]),\\n /**\\n * The variant to use.\\n * @default \'regular\'\\n */\\n variant: PropTypes /* @typescript-to-proptypes-ignore */.oneOfType([PropTypes.oneOf([\'dense\', \'regular\']), PropTypes.string])\\n} : void 0;\\nexport default Toolbar;","import generateUtilityClasses from \'@mui/utils/generateUtilityClasses\';\\nimport generateUtilityClass from \'@mui/utils/generateUtilityClass\';\\nexport function getToolbarUtilityClass(slot) {\\n return generateUtilityClass(\'MuiToolbar\', slot);\\n}\\nconst toolbarClasses = generateUtilityClasses(\'MuiToolbar\', [\'root\', \'gutters\', \'regular\', \'dense\']);\\nexport default toolbarClasses;"],"names":["circularRotateKeyframe","circularDashKeyframe","rotateAnimation","dashAnimation","CircularProgressRoot","name","slot","overridesResolver","props","styles","ownerState","root","variant","color","theme","display","variants","style","transition","transitions","create","animation","Object","entries","palette","filter","map","vars","main","CircularProgressSVG","svg","CircularProgressCircle","circle","disableShrink","circleDisableShrink","stroke","strokeDasharray","strokeDashoffset","inProps","ref","className","size","thickness","value","other","classes","slots","useUtilityClasses","circleStyle","rootStyle","rootProps","circumference","Math","PI","toFixed","round","transform","width","height","role","children","viewBox","cx","cy","r","fill","strokeWidth","getCircularProgressUtilityClass","mapEventPropToEvent","eventProp","substring","toLowerCase","ClickAwayListener","disableReactTree","mouseEvent","onClickAway","touchEvent","movedRef","nodeRef","activatedRef","syntheticEventRef","setTimeout","current","handleRef","handleClickAway","event","insideReactTree","doc","documentElement","clientWidth","clientX","clientHeight","clientY","clickedRootScrollbar","insideDOM","composedPath","includes","contains","target","createHandleSynthetic","handlerName","childrenPropsHandler","childrenProps","mappedTouchEvent","handleTouchMove","addEventListener","removeEventListener","mappedMouseEvent","ToolbarRoot","disableGutters","gutters","position","alignItems","paddingLeft","spacing","paddingRight","breakpoints","up","minHeight","mixins","toolbar","component","as","getToolbarUtilityClass"],"sourceRoot":""}\n\\ No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/8343.dd515382.chunk.js
--- a/x/static/js/8343.dd515382.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8343.dd515382.chunk.js.map
--- a/x/static/js/8343.dd515382.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8408.2e2896bf.chunk.js
--- a/x/static/js/8408.2e2896bf.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8408.2e2896bf.chunk.js.map
--- a/x/static/js/8408.2e2896bf.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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(\n <BlockMsg\n message={`${error}`}\n severity=\"error\"\n action={\n <Tooltip title=\"Reload\">\n <Button\n data-testid=\"reload_button\"\n onClick={() => {\n model.reload()\n }}\n >\n Reload\n </Button>\n </Tooltip>\n }\n />\n ) : regionTooLarge ? (\n model.regionCannotBeRendered()\n ) : (\n <DataDisplay model={model}>{children}</DataDisplay>\n )\n})\n\nconst DataDisplay = observer(function ({\n model,\n children,\n}: {\n model: LinearReadArcsDisplayModel | LinearReadCloudDisplayModel\n children?: React.ReactNode\n}) {\n const { drawn, loading } = model\n const view = getContainingView(model) as LinearGenomeViewModel\n const left = (model.lastDrawnOffsetPx || 0) - view.offsetPx\n return (\n // this data-testid is located here because changing props on the canvas\n // itself is very sensitive to triggering ref invalidation\n <div data-testid={`drawn-${drawn}`}>\n <div style={{ position: 'absolute', left }}>{children}</div>\n {left !== 0 || loading ? <LoadingBar model={model} /> : null}\n </div>\n )\n})\n\nconst LoadingBar = observer(function ({\n model,\n}: {\n model: LinearReadArcsDisplayModel | LinearReadCloudDisplayModel\n}) {\n const { classes } = useStyles()\n const { message } = model\n return (\n <div className={classes.loading}>\n <LoadingEllipses message={message} />\n </div>\n )\n})\n\nexport default BaseDisplayComponent\n"],"names":["Cloud","observer","model","view","getContainingView","width","Math","round","dynamicBlocks","totalWidthPx","height","cb","useCallback","ref","setRef","React","style","position","BaseDisplayComponent","useStyles","makeStyles","theme","loading","backgroundColor","palette","background","default","backgroundImage","action","disabledBackground","bottom","right","pointerEvents","textAlign","children","error","regionTooLarge","BlockMsg","message","severity","Tooltip","title","Button","onClick","reload","regionCannotBeRendered","DataDisplay","drawn","left","lastDrawnOffsetPx","offsetPx","LoadingBar","classes","className","LoadingEllipses"],"sourceRoot":""}
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8424.a1a3e663.chunk.js
--- a/x/static/js/8424.a1a3e663.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8424.a1a3e663.chunk.js.map
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factor <= sqrtN; factor++) {\\n\\t if (!(n % factor)) {\\n\\t return false;\\n\\t }\\n\\t }\\n\\n\\t return true;\\n\\t }\\n\\n\\t function getFractionalBits(n) {\\n\\t return ((n - (n | 0)) * 0x100000000) | 0;\\n\\t }\\n\\n\\t var n = 2;\\n\\t var nPrime = 0;\\n\\t while (nPrime < 64) {\\n\\t if (isPrime(n)) {\\n\\t if (nPrime < 8) {\\n\\t H[nPrime] = getFractionalBits(Math.pow(n, 1 / 2));\\n\\t }\\n\\t K[nPrime] = getFractionalBi'..b' ((gamma0x << 14) | (gamma0x >>> 18)) ^\\n\\t (gamma0x >>> 3);\\n\\n\\t var gamma1x = W[i - 2];\\n\\t var gamma1 = ((gamma1x << 15) | (gamma1x >>> 17)) ^\\n\\t ((gamma1x << 13) | (gamma1x >>> 19)) ^\\n\\t (gamma1x >>> 10);\\n\\n\\t W[i] = gamma0 + W[i - 7] + gamma1 + W[i - 16];\\n\\t }\\n\\n\\t var ch = (e & f) ^ (~e & g);\\n\\t var maj = (a & b) ^ (a & c) ^ (b & c);\\n\\n\\t var sigma0 = ((a << 30) | (a >>> 2)) ^ ((a << 19) | (a >>> 13)) ^ ((a << 10) | (a >>> 22));\\n\\t var sigma1 = ((e << 26) | (e >>> 6)) ^ ((e << 21) | (e >>> 11)) ^ ((e << 7) | (e >>> 25));\\n\\n\\t var t1 = h + sigma1 + ch + K[i] + W[i];\\n\\t var t2 = sigma0 + maj;\\n\\n\\t h = g;\\n\\t g = f;\\n\\t f = e;\\n\\t e = (d + t1) | 0;\\n\\t d = c;\\n\\t c = b;\\n\\t b = a;\\n\\t a = (t1 + t2) | 0;\\n\\t }\\n\\n\\t // Intermediate hash value\\n\\t H[0] = (H[0] + a) | 0;\\n\\t H[1] = (H[1] + b) | 0;\\n\\t H[2] = (H[2] + c) | 0;\\n\\t H[3] = (H[3] + d) | 0;\\n\\t H[4] = (H[4] + e) | 0;\\n\\t H[5] = (H[5] + f) | 0;\\n\\t H[6] = (H[6] + g) | 0;\\n\\t H[7] = (H[7] + h) | 0;\\n\\t },\\n\\n\\t _doFinalize: function () {\\n\\t // Shortcuts\\n\\t var data = this._data;\\n\\t var dataWords = data.words;\\n\\n\\t var nBitsTotal = this._nDataBytes * 8;\\n\\t var nBitsLeft = data.sigBytes * 8;\\n\\n\\t // Add padding\\n\\t dataWords[nBitsLeft >>> 5] |= 0x80 << (24 - nBitsLeft % 32);\\n\\t dataWords[(((nBitsLeft + 64) >>> 9) << 4) + 14] = Math.floor(nBitsTotal / 0x100000000);\\n\\t dataWords[(((nBitsLeft + 64) >>> 9) << 4) + 15] = nBitsTotal;\\n\\t data.sigBytes = dataWords.length * 4;\\n\\n\\t // Hash final blocks\\n\\t this._process();\\n\\n\\t // Return final computed hash\\n\\t return this._hash;\\n\\t },\\n\\n\\t clone: function () {\\n\\t var clone = Hasher.clone.call(this);\\n\\t clone._hash = this._hash.clone();\\n\\n\\t return clone;\\n\\t }\\n\\t });\\n\\n\\t /**\\n\\t * Shortcut function to the hasher\'s object interface.\\n\\t *\\n\\t * @param {WordArray|string} message The message to hash.\\n\\t *\\n\\t * @return {WordArray} The hash.\\n\\t *\\n\\t * @static\\n\\t *\\n\\t * @example\\n\\t *\\n\\t * var hash = CryptoJS.SHA256(\'message\');\\n\\t * var hash = CryptoJS.SHA256(wordArray);\\n\\t */\\n\\t C.SHA256 = Hasher._createHelper(SHA256);\\n\\n\\t /**\\n\\t * Shortcut function to the HMAC\'s object interface.\\n\\t *\\n\\t * @param {WordArray|string} message The message to hash.\\n\\t * @param {WordArray|string} key The secret key.\\n\\t *\\n\\t * @return {WordArray} The HMAC.\\n\\t *\\n\\t * @static\\n\\t *\\n\\t * @example\\n\\t *\\n\\t * var hmac = CryptoJS.HmacSHA256(message, key);\\n\\t */\\n\\t C.HmacSHA256 = Hasher._createHmacHelper(SHA256);\\n\\t}(Math));\\n\\n\\n\\treturn CryptoJS.SHA256;\\n\\n}));"],"names":["CryptoJS","module","exports","Math","C","C_lib","lib","WordArray","Hasher","C_algo","algo","H","K","isPrime","n","sqrtN","sqrt","factor","getFractionalBits","nPrime","pow","W","SHA256","extend","_doReset","this","_hash","init","slice","_doProcessBlock","M","offset","words","a","b","c","d","e","f","g","h","i","gamma0x","gamma0","gamma1x","gamma1","maj","sigma0","t1","_doFinalize","data","_data","dataWords","nBitsTotal","_nDataBytes","nBitsLeft","sigBytes","floor","length","_process","clone","call","_createHelper","HmacSHA256","_createHmacHelper"],"sourceRoot":""}\n\\ No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/8435.484d30f8.chunk.js
--- a/x/static/js/8435.484d30f8.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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b'@@ -1,2 +0,0 @@\n-"use strict";(globalThis.webpackChunk_jbrowse_web=globalThis.webpackChunk_jbrowse_web||[]).push([[8435],{48435:(n,e,a)=>{a.d(e,{doConnect:()=>L});class t{constructor(n=[],e){this.data={};const{checkIndent:a=!0,skipValidation:t=!1}=null!=e?e:{};let r,i,o;r="string"==typeof n?n.trimEnd().split(/\\r?\\n/):n||[];for(const n of r){if(""===n)throw new Error("Invalid stanza, contained blank lines");if(n.trim().startsWith("#"))continue;if(n.trimEnd().endsWith("\\\\")){const e=n.trimEnd().slice(0,-1);o?o+=e.trimStart():o=e;continue}let e=n;if(o&&(e=o+e.trimStart(),o=void 0),null!=i?i:a){const n=e.match(/^([ \\t]+)/);if(void 0===i)n?[,i]=n:i="";else if(""===i&&null!==n||i&&n&&i!==n[1])throw new Error("Inconsistent indentation of stanza")}else i="";const t=e.trim(),r=t.indexOf(" ");if(-1===r){if(!this.nameKey)throw new Error("First line in a stanza must have both a key and a value");if(this.data[t])continue;this.data[t]="";continue}const s=t.slice(0,r),c=t.slice(r+1);if(this.data[s]&&c!==this.data[s])throw new Error(`Got duplicate key with a different value in stanza: "${s}" key has both ${this.data[s]} and ${c}`);this.nameKey||(this.nameKey=s,this.name=t.slice(r+1)),this.data[s]=c}t||this.validate()}validate(){}}class r{constructor(n=[],e){this.data={};const{checkIndent:a=!0,skipValidation:r=!1}=null!=e?e:{};let i;i="string"==typeof n?n.trimEnd().split(/(?:[\\t ]*\\r?\\n){2,}/):n||[];for(const n of i){if(""===n)throw new Error("Invalid stanza, was empty");if(n.trim().startsWith("#")&&n.trimEnd().split(/\\r?\\n/).map((n=>n.trim())).every((n=>n.startsWith("#"))))continue;const e=new t(n,{checkIndent:a});if(this.nameKey){if(e.nameKey!==this.nameKey)throw new Error(`The first line in each stanza must have the same key. 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l{constructor(n){const[e,a,...r]=n.trimEnd().split(/(?:[\\t ]*\\r?\\n){2,}/);this.hubData=new t(e),this.validateHub(),this.genome=new t(a),this.validateGenomeSection(),this.tracks=new o(r.join("\\n\\n"),{skipValidation:!1})}validateHub(){if("hub"!==this.hubData.nameKey)throw new Error(\'Hub file must begin with a line like "hub 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y=a(68584),w=a(32761);function k(n,e){return new URL(n,e).href}async function L(n){const e=(0,d.getSession)(n),a=[];try{const t=(0,y.getConf)(n,"hubTxtLocation"),r=await(0,h.openLocation)(t).readFile("utf8"),i=k(t.uri,t.baseUri),{assemblyManager:o}=e;if(r.includes("useOneFile on")){const a=new l(r),{genome:s,tracks:c}=a,d=s.name;o.get(d)||e.addSessionAssembly({name:d,sequence:{type:"ReferenceSequenceTrack",trackId:`${d}-${(0,w.Ak)()}`,adapter:{type:"TwoBitAdapter",twoBitLocation:{uri:k(s.data.twoBitPath,i)},chromSizesLocation:{uri:k(s.data.chromSizes,i)}}}});const h=o.get(d),m=g({trackDb:c,trackDbLoc:t,assemblyName:d,sequenceAdapter:(0,y.getConf)(h,["sequence","adapter"])});n.addTrackConfs(m)}else{const i=new c(r).data.genomesFile;if(!i)throw new Error("genomesFile not found on hub");const l=k(t.uri,t.baseUri),d=l?{uri:k(i,l),locationType:"UriLocation"}:{localPath:i,locationType:"LocalPathLocation"},m=await async function(n){const e=await(0,h.openLocation)(n).readFile("utf8");return new s(e)}(d),p={};for(const[e,t]of Object.entries(m.data)){const r=(0,y.getConf)(n,"assemblyNames");if(r.length>0&&!r.includes(e))continue;const s=o.get(e);if(!s){a.push(e);continue}const c=t.data.trackDb;if(!c)throw new Error("genomesFile not found on hub");const d=new URL(i,l),h=l?{uri:new URL(c,d).href,locationType:"UriLocation"}:{localPath:c,locationType:"LocalPathLocation"},m=g({trackDb:await u(h),trackDbLoc:h,assemblyName:e,sequenceAdapter:(0,y.getConf)(s,["sequence","adapter"])});n.addTrackConfs(m),p[e]=m.length}const b=Object.entries(p),f=b.length?`Loaded data from these assemblies: ${b.map((([n,e])=>`${n} (${e} tracks)`)).join(", ")}`:"",w=a.length?`Skipped data from these assemblies: ${a.join(", ")}`:"";e.notify([f,w].filter((n=>!!n)).join(". 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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8435.484d30f8.chunk.js.map
--- a/x/static/js/8435.484d30f8.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8483.7fadf4ea.chunk.js
--- a/x/static/js/8483.7fadf4ea.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8483.7fadf4ea.chunk.js.map
--- a/x/static/js/8483.7fadf4ea.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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CardActionArea.propTypes /* remove-proptypes */ = {\n // ┌────────────────────────────── Warning ──────────────────────────────┐\n // │ These PropTypes are generated from the TypeScript type definitions. │\n // │ To update them, edit the d.ts file and run `pnpm proptypes`. │\n // └─────────────────────────────────────────────────────────────────────┘\n /**\n * The content of the component.\n */\n children: PropTypes.node,\n /**\n * Override or extend the styles applied to the component.\n */\n classes: PropTypes.object,\n /**\n * @ignore\n */\n className: PropTypes.string,\n /**\n * @ignore\n */\n focusVisibleClassName: PropTypes.string,\n /**\n * The system prop that allows defining system overrides as well as additional CSS styles.\n */\n sx: PropTypes.oneOfType([PropTypes.arrayOf(PropTypes.oneOfType([PropTypes.func, PropTypes.object, PropTypes.bool])), PropTypes.func, PropTypes.object])\n} : void 0;\nexport default CardActionArea;"],"names":["getCardActionAreaUtilityClass","slot","generateUtilityClass","generateUtilityClasses","CardActionAreaRoot","styled","ButtonBase","name","overridesResolver","props","styles","root","memoTheme","theme","display","textAlign","borderRadius","width","focusHighlight","opacity","vars","palette","action","hoverOpacity","focusVisible","focusOpacity","CardActionAreaFocusHighlight","overflow","pointerEvents","position","top","right","bottom","left","backgroundColor","transition","transitions","create","duration","short","inProps","ref","children","className","focusVisibleClassName","other","ownerState","classes","composeClasses","useUtilityClasses","clsx"],"sourceRoot":""}
\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/static/js/8526.5dd9c712.chunk.js
--- a/x/static/js/8526.5dd9c712.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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--- a/x/static/js/8528.f68ff14f.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8535.189d090a.chunk.js
--- a/x/static/js/8535.189d090a.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8535.189d090a.chunk.js.map
--- a/x/static/js/8535.189d090a.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8546.0a89cbee.chunk.js
--- a/x/static/js/8546.0a89cbee.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8546.0a89cbee.chunk.js.map
--- a/x/static/js/8546.0a89cbee.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8556.0053a402.chunk.js
--- a/x/static/js/8556.0053a402.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8556.0053a402.chunk.js.map
--- a/x/static/js/8556.0053a402.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8565.c4ea9980.chunk.js
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8624.190dd7af.chunk.js
--- a/x/static/js/8624.190dd7af.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8624.190dd7af.chunk.js.map
--- a/x/static/js/8624.190dd7af.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8678.8424d5dc.chunk.js
--- a/x/static/js/8678.8424d5dc.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8678.8424d5dc.chunk.js.map
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No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/8704.ae4808df.chunk.js
--- a/x/static/js/8704.ae4808df.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8704.ae4808df.chunk.js.map
--- a/x/static/js/8704.ae4808df.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8762.3d2b9142.chunk.js
--- a/x/static/js/8762.3d2b9142.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8762.3d2b9142.chunk.js.map
--- a/x/static/js/8762.3d2b9142.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8797.3168365d.chunk.js
--- a/x/static/js/8797.3168365d.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8797.3168365d.chunk.js.map
--- a/x/static/js/8797.3168365d.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8856.4593419f.chunk.js
--- a/x/static/js/8856.4593419f.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8856.4593419f.chunk.js.map
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--- a/x/static/js/8859.efb2561f.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8859.efb2561f.chunk.js.map
--- a/x/static/js/8859.efb2561f.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8869.74066774.chunk.js
--- a/x/static/js/8869.74066774.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/static/js/8869.74066774.chunk.js.map
--- a/x/static/js/8869.74066774.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8876.24bf6aed.chunk.js
--- a/x/static/js/8876.24bf6aed.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8876.24bf6aed.chunk.js.map
--- a/x/static/js/8876.24bf6aed.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8880.6ae9d985.chunk.js
--- a/x/static/js/8880.6ae9d985.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8880.6ae9d985.chunk.js.map
--- a/x/static/js/8880.6ae9d985.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8929.70ce258f.chunk.js
--- a/x/static/js/8929.70ce258f.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,2 +0,0 @@
-"use strict";(globalThis.webpackChunk_jbrowse_web=globalThis.webpackChunk_jbrowse_web||[]).push([[8929],{98929:(t,e,n)=>{n.r(e),n.d(e,{default:()=>l});var a=n(99834),s=n(99546),i=n(7706),o=n(35904);const r="undefined"!=typeof TextDecoder?new TextDecoder("utf8"):void 0;function c(t,e,n,a,s,i,o,r,c){return{qname:t,qstart:e,qend:n,tname:s,tstart:i,tend:o,strand:"-"===a?-1:1,extra:{numMatches:c,blockLen:Math.max(n-e,o-i),mappingQual:0,cg:r}}}class l extends o.default{async setupPre(t){const e=(0,a.openLocation)(this.getConf("chainLocation"),this.pluginManager),n=await e.readFile(t);return function(t){let e="",n=0,a=0,s="",i="",o="",l=0,u=0,d=0,h="";const p=[];let f=0;for(;f<t.length;){const b=t.indexOf("\n",f);if(-1===b)break;const g=t.subarray(f,b);f=b+1;const w=(r?.decode(g)||g.toString()).trim().replaceAll(" ","\t").split("\t");if("chain"===w[0]){if(h&&p.push(c(s,l,u,o,e,n,a,h,d)),e=w[2],n=+w[5],a=+w[6],s=w[7],i=w[8],o=w[9],l=+w[10],u=+w[11],"-"===o){const t=l;l=+i-u,u=+i-t}d=0,h=""}else{const t=+w[0]||0,e=w.length>1?+w[1]:0,n=w.length>2?+w[2]:0;0!==t&&(d+=+t,h+=`${t}M`),0!==n&&(h+=`${n}I`),0!==e&&(h+=`${e}D`)}}return h&&c(s,l,u,o,e,n,a,h,d),p}((0,s.isGzip)(n)?await(0,i.unzip)(n):n)}}}}]);
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8929.70ce258f.chunk.js.map
--- a/x/static/js/8929.70ce258f.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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IN NO EVENT SHALL THE\\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\\n * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE\\n * SOFTWARE.\\n */\\n\\nfunction generate_record(\\n qname: string,\\n qstart: number,\\n qend: number,\\n qstrand: string,\\n tname: string,\\n tstart: number,\\n tend: number,\\n cigar: string,\\n numMatches: number,\\n) {\\n return {\\n qname,\\n qstart,\\n qend,\\n tname,\\n tstart,\\n tend,\\n strand: qstrand === \'-\' ? -1 : 1,\\n extra: {\\n numMatches,\\n blockLen: Math.max(qend - qstart, tend - tstart),\\n mappingQual: 0,\\n cg: cigar,\\n },\\n }\\n}\\n\\nexport function paf_chain2paf(buffer: Buffer) {\\n let t_name = \'\'\\n let t_start = 0\\n let t_end = 0\\n let q_name = \'\'\\n let q_size = \'\'\\n let q_strand = \'\'\\n let q_start = 0\\n let q_end = 0\\n let num_matches = 0\\n let cigar = \'\'\\n const records = []\\n\\n let blockStart = 0\\n while (blockStart < buffer.length) {\\n '..b'e-separated fields\\n const l_vec = l_tab.split(\'\\\\t\')\\n\\n if (l_vec[0] === \'chain\') {\\n // Emit previous PAF row, if available\\n if (cigar) {\\n records.push(\\n generate_record(\\n q_name,\\n q_start,\\n q_end,\\n q_strand,\\n t_name,\\n t_start,\\n t_end,\\n cigar,\\n num_matches,\\n ),\\n )\\n }\\n\\n // Save query/target information\\n // score -- chain score\\n // tName -- chromosome (reference sequence)\\n // tSize -- chromosome size (reference sequence)\\n // tStrand -- strand (reference sequence)\\n // tStart -- alignment start position (reference sequence)\\n // tEnd -- alignment end position (reference sequence)\\n // qName -- chromosome (query sequence)\\n // qSize -- chromosome size (query sequence)\\n // qStrand -- strand (query sequence)\\n // qStart -- alignment start position (query sequence)\\n // qEnd -- alignment end position (query sequence)\\n // id -- chain ID\\n t_name = l_vec[2]!\\n t_start = +l_vec[5]!\\n t_end = +l_vec[6]!\\n q_name = l_vec[7]!\\n q_size = l_vec[8]!\\n q_strand = l_vec[9]!\\n q_start = +l_vec[10]!\\n q_end = +l_vec[11]!\\n if (q_strand === \'-\') {\\n const tmp = q_start\\n q_start = +q_size - q_end\\n q_end = +q_size - tmp\\n }\\n\\n // Initialize PAF fields\\n num_matches = 0\\n cigar = \'\'\\n } else {\\n // size -- the size of the ungapped alignment\\n //\\n // dt -- the difference between the end of this block and the beginning\\n // of the next block (reference sequence)\\n //\\n // dq -- the difference between the end of this block and the beginning\\n // of the next block (query sequence)\\n const size_ungapped_alignment = +l_vec[0]! || 0\\n const diff_in_target = l_vec.length > 1 ? +l_vec[1]! : 0\\n const diff_in_query = l_vec.length > 2 ? +l_vec[2]! : 0\\n\\n if (size_ungapped_alignment !== 0) {\\n num_matches += +size_ungapped_alignment\\n cigar += `${size_ungapped_alignment}M`\\n }\\n if (diff_in_query !== 0) {\\n cigar += `${diff_in_query}I`\\n }\\n if (diff_in_target !== 0) {\\n cigar += `${diff_in_target}D`\\n }\\n }\\n }\\n\\n // Emit last PAF row, if available\\n if (cigar) {\\n generate_record(\\n q_name,\\n q_start,\\n q_end,\\n q_strand,\\n t_name,\\n t_start,\\n t_end,\\n cigar,\\n num_matches,\\n )\\n }\\n return records\\n}\\n","import { BaseOptions } from \'@jbrowse/core/data_adapters/BaseAdapter\'\\nimport { openLocation } from \'@jbrowse/core/util/io\'\\nimport { isGzip } from \'@jbrowse/core/util\'\\nimport { unzip } from \'@gmod/bgzf-filehandle\'\\nimport type { Buffer } from \'buffer\'\\n\\n// locals\\nimport PAFAdapter from \'../PAFAdapter/PAFAdapter\'\\nimport { paf_chain2paf } from \'./util\'\\n\\nexport default class ChainAdapter extends PAFAdapter {\\n async setupPre(opts?: BaseOptions) {\\n const loc = openLocation(this.getConf(\'chainLocation\'), this.pluginManager)\\n const buffer = (await loc.readFile(opts)) as Buffer\\n const buf = isGzip(buffer) ? await unzip(buffer) : buffer\\n return paf_chain2paf(buf)\\n }\\n}\\n"],"names":["decoder","TextDecoder","undefined","generate_record","qname","qstart","qend","qstrand","tname","tstart","tend","cigar","numMatches","strand","extra","blockLen","Math","max","mappingQual","cg","ChainAdapter","PAFAdapter","setupPre","opts","loc","openLocation","this","getConf","pluginManager","buffer","readFile","t_name","t_start","t_end","q_name","q_size","q_strand","q_start","q_end","num_matches","records","blockStart","length","n","indexOf","b","subarray","l_vec","decode","toString","trim","replaceAll","split","push","tmp","size_ungapped_alignment","diff_in_target","diff_in_query","paf_chain2paf","isGzip","unzip"],"sourceRoot":""}\n\\ No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/8965.51db703f.chunk.js
--- a/x/static/js/8965.51db703f.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8965.51db703f.chunk.js.map
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/8984.1a816123.chunk.js
--- a/x/static/js/8984.1a816123.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9032.b54e1975.chunk.js
--- a/x/static/js/9032.b54e1975.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9032.b54e1975.chunk.js.map
--- a/x/static/js/9032.b54e1975.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9037.03715b7f.chunk.js
--- a/x/static/js/9037.03715b7f.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9067.1cc02121.chunk.js
--- a/x/static/js/9067.1cc02121.chunk.js Fri Oct 18 11:57:55 2024 +0000
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No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/9070.d49de235.chunk.js
--- a/x/static/js/9070.d49de235.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9070.d49de235.chunk.js.map
--- a/x/static/js/9070.d49de235.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/static/js/9086.035adaa3.chunk.js
--- a/x/static/js/9086.035adaa3.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9086.035adaa3.chunk.js.map
--- a/x/static/js/9086.035adaa3.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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count: counts,\\n maxScore,\\n baseColor,\\n scale,\\n useLogScale,\\n })\\n ctx.fillRect((bin1 - offset) * w, (bin2 - offset) * w, w, w)\\n if (+Date.now() - start > 400) {\\n await abortBreakPoint(signal)\\n start = +Date.now()\\n }\\n }\\n ctx.restore()\\n }\\n return undefined\\n}\\n"],"names":["transformer","t0","t1","k10","transform","unknown","x0","x1","interpolator","clamp","scale","x","isNaN","Math","max","min","range","interpolate","_","r0","r1","arguments","length","domain","rangeRound","t","copy","source","target","sequential","linear","init","apply","sequentialLog","log","base","n","floor","specifier","colors","Array","i","slice","async","makeImageData","ctx","props","features","config","bpPerPx","signal","resolution","sessionId","adapterConfig","useLogScale","colorScheme","regions","pluginManager","region","dataAdapter","getAdapter","res","getResolution","width","end","start","w","sqrt","baseColor","colord","readConfObject","offset","maxScore","minBin","maxBin","abortBreakPoint","bin1","bin2","counts","colorSchemes","juicebox","fall","interpolateRgbBasis","viridis","interpolateViridis","m","scaleSequentialLog","scaleSequential","save","reversed","translate","rotate","PI","Date","now","fillStyle","count","fillRect","restore"],"sourceRoot":""}\n\\ No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/9106.b274c701.chunk.js
--- a/x/static/js/9106.b274c701.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9106.b274c701.chunk.js.map
--- a/x/static/js/9106.b274c701.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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ListItemSecondaryAction.propTypes /* remove-proptypes */ = {\\n // \xe2\x94\x8c\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80 Warning \xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x90\\n // \xe2\x94\x82 These PropTypes are generated from the TypeScript type definitions. \xe2\x94\x82\\n // \xe2\x94\x82 To update them, edit the d.ts file and run `pnpm proptypes`. 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/**\\n * Override or extend the styles applied to the component.\\n */\\n classes: PropTypes.object,\\n /**\\n * @ignore\\n */\\n className: PropTypes.string,\\n /**\\n * The system prop that allows defining system overrides as well as additional CSS styles.\\n */\\n sx: PropTypes.oneOfType([PropTypes.arrayOf(PropTypes.oneOfType([PropTypes.func, PropTypes.object, PropTypes.bool])), PropTypes.func, PropTypes.object])\\n} : void 0;\\nListItemSecondaryAction.muiName = \'ListItemSecondaryAction\';\\nexport default ListItemSecondaryAction;","import generateUtilityClasses from \'@mui/utils/generateUtilityClasses\';\\nimport generateUtilityClass from \'@mui/utils/generateUtilityClass\';\\nexport function getListItemSecondaryActionClassesUtilityClass(slot) {\\n return generateUtilityClass(\'MuiListItemSecondaryAction\', slot);\\n}\\nconst listItemSecondaryActionClasses = generateUtilityClasses(\'MuiListItemSecondaryAction\', [\'root\', \'disableGutters\']);\\nexport default 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No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/9114.d412d44e.chunk.js
--- a/x/static/js/9114.d412d44e.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,2 +0,0 @@
-"use strict";(globalThis.webpackChunk_jbrowse_web=globalThis.webpackChunk_jbrowse_web||[]).push([[9114],{9114:(e,t,a)=>{a.r(t),a.d(t,{default:()=>c});var n=a(7552),l=a(68984),r=a(99546),i=a(36715),s=a(87731);const u=(0,n.lazy)((()=>a.e(5930).then(a.bind(a,45930)))),o=(0,n.lazy)((()=>a.e(457).then(a.bind(a,80457))));function m({model:e,feature:t,viewType:a}){const l=(0,r.getSession)(e),m={uniqueId:t.uniqueId,refName:t.refName,start:t.start,end:t.end,strand:t.strand},d={uniqueId:`${t.id}-mate`,refName:t.next_ref,start:t.next_pos,end:t.next_pos+1,strand:t.strand};return n.createElement("div",null,n.createElement(i.A,null,"Launch split view"),n.createElement("ul",null,n.createElement("li",null,m.refName,":",(0,r.toLocale)(m.start)," -> ",d.refName,":",(0,r.toLocale)(d.start)," ",n.createElement(s.A,{href:"#",onClick:t=>{t.preventDefault(),l.queueDialog((t=>[u,{handleClose:t,model:e,feature:new r.SimpleFeature({...m,mate:d}),viewType:a,view:e.view,assemblyName:e.view.displayedRegions[0].assemblyName}]))}},"(top/bottom)")," ",n.createElement(s.A,{href:"#",onClick:t=>{t.preventDefault(),l.queueDialog((t=>[o,{handleClose:t,model:e,feature:new r.SimpleFeature({...m,mate:d}),viewType:a,view:e.view,assemblyName:e.view.displayedRegions[0].assemblyName}]))}},"(single row)"))))}function d(){return d=Object.assign?Object.assign.bind():function(e){for(var t=1;t<arguments.length;t++){var a=arguments[t];for(var n in a)({}).hasOwnProperty.call(a,n)&&(e[n]=a[n])}return e},d.apply(null,arguments)}function c(e){const{model:t,feature:a}=e,i=(0,r.getSession)(t),{pluginManager:s}=(0,r.getEnv)(i);let u;try{u=s.getViewType("BreakpointSplitView")}catch(e){}return n.createElement(l.BaseCard,d({},e,{title:"Supplementary alignments"}),u?n.createElement(m,{viewType:u,model:t,feature:a}):null)}}}]);
-//# sourceMappingURL=9114.d412d44e.chunk.js.map
\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/static/js/9114.d412d44e.chunk.js.map
--- a/x/static/js/9114.d412d44e.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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(\n <LaunchPairedEndBreakpointSplitViewPanel\n viewType={viewType}\n model={model}\n feature={feature}\n />\n ) : null}\n </BaseCard>\n )\n}\n"],"names":["BreakendMultiLevelOptionDialog","lazy","BreakendSingleLevelOptionDialog","LaunchPairedEndBreakpointSplitViewPanel","model","feature","viewType","session","getSession","f1","uniqueId","refName","start","end","strand","f2","id","next_ref","next_pos","React","Typography","toLocale","Link","href","onClick","event","preventDefault","queueDialog","handleClose","SimpleFeature","mate","view","assemblyName","displayedRegions","SuppAlignments","props","pluginManager","getEnv","getViewType","e","BaseCard","_extends","title"],"sourceRoot":""}
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9168.6afdec67.chunk.js
--- a/x/static/js/9168.6afdec67.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9168.6afdec67.chunk.js.map
--- a/x/static/js/9168.6afdec67.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/9206.bbf34514.chunk.js
--- a/x/static/js/9206.bbf34514.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,2 +0,0 @@
-"use strict";(globalThis.webpackChunk_jbrowse_web=globalThis.webpackChunk_jbrowse_web||[]).push([[9206,7489],{79206:(e,t,a)=>{a.r(t),a.d(t,{default:()=>o});var s=a(71616),n=a(99834),i=a(69870);class o extends i.default{async setupPre(){const e=this.getConf("fastaLocation"),t=this.getConf("faiLocation"),a=this.getConf("gziLocation"),i={fasta:(0,n.openLocation)(e,this.pluginManager),fai:(0,n.openLocation)(t,this.pluginManager),gzi:(0,n.openLocation)(a,this.pluginManager)};return{fasta:new s.tP(i)}}}},69870:(e,t,a)=>{a.r(t),a.d(t,{default:()=>f});var s=a(71616),n=a(46377),i=a(99834),o=a(66885),r=a(99546),c=a(47046),u=a(43334);class f extends n.BaseSequenceAdapter{seqCache=new c.A({cache:new u.A({maxSize:200}),fill:async(e,t)=>{const{refName:a,start:s,end:n,fasta:i}=e;return i.getSequence(a,s,n,{...e,signal:t})}});async getRefNames(e){const{fasta:t}=await this.setup();return t.getSequenceNames(e)}async getRegions(e){const{fasta:t}=await this.setup(),a=await t.getSequenceSizes(e);return Object.keys(a).map((e=>({refName:e,start:0,end:a[e]})))}async setupPre(){const e=this.getConf("fastaLocation"),t=this.getConf("faiLocation");return{fasta:new s.BL({fasta:(0,i.openLocation)(e,this.pluginManager),fai:(0,i.openLocation)(t,this.pluginManager)})}}async getHeader(){const e=this.getConf("metadataLocation");return""===e.uri||"/path/to/fa.metadata.yaml"===e.uri?null:(0,i.openLocation)(e,this.pluginManager).readFile("utf8")}async setup(){return this.setupP||(this.setupP=this.setupPre().catch((e=>{throw this.setupP=void 0,e}))),this.setupP}getFeatures(e,t){const{refName:a,start:s,end:n}=e;return(0,o.ObservableCreate)((async e=>{const{fasta:i}=await this.setup(),o=await i.getSequenceSize(a,t),c=Math.min(o,n),u=[],f=128e3,g=s-s%f,h=n+(f-n%f);for(let e=g;e<h;e+=f){const s={refName:a,start:e,end:e+f};u.push(this.seqCache.get(JSON.stringify(s),{...s,fasta:i},t?.signal))}const p=(await Promise.all(u)).join("").slice(s-g).slice(0,n-s);p&&e.next(new r.SimpleFeature({id:`${a} ${s}-${c}`,data:{refName:a,start:s,end:c,seq:p}})),e.complete()}))}freeResources(){}}}}]);
-//# sourceMappingURL=9206.bbf34514.chunk.js.map
\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/static/js/9206.bbf34514.chunk.js.map
--- a/x/static/js/9206.bbf34514.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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null\n : openLocation(loc, this.pluginManager).readFile('utf8')\n }\n\n public async setup() {\n if (!this.setupP) {\n this.setupP = this.setupPre().catch((e: unknown) => {\n this.setupP = undefined\n throw e\n })\n }\n return this.setupP\n }\n\n public getFeatures(region: NoAssemblyRegion, opts?: BaseOptions) {\n const { refName, start, end } = region\n return ObservableCreate<Feature>(async observer => {\n const { fasta } = await this.setup()\n const size = await fasta.getSequenceSize(refName, opts)\n const regionEnd = Math.min(size, end)\n const chunks = []\n const chunkSize = 128000\n\n const s = start - (start % chunkSize)\n const e = end + (chunkSize - (end % chunkSize))\n for (let chunkStart = s; chunkStart < e; chunkStart += chunkSize) {\n const r = {\n refName,\n start: chunkStart,\n end: chunkStart + chunkSize,\n }\n chunks.push(\n this.seqCache.get(JSON.stringify(r), { ...r, fasta }, opts?.signal),\n )\n }\n const seq = (await Promise.all(chunks))\n .join('')\n .slice(start - s)\n .slice(0, end - start)\n if (seq) {\n observer.next(\n new SimpleFeature({\n id: `${refName} ${start}-${regionEnd}`,\n data: { refName, start, end: regionEnd, seq },\n }),\n )\n }\n observer.complete()\n })\n }\n\n /**\n * called to provide a hint that data tied to a certain region\n * will not be needed for the foreseeable future and can be purged\n * from caches, etc\n */\n public freeResources(/* { region } */): void {}\n}\n"],"names":["BgzipFastaAdapter","IndexedFasta","setupPre","fastaLocation","this","getConf","faiLocation","gziLocation","fastaOpts","fasta","openLocation","pluginManager","fai","gzi","BgzipIndexedFasta","IndexedFastaAdapter","BaseSequenceAdapter","seqCache","AbortablePromiseCache","cache","QuickLRU","maxSize","fill","async","args","signal","refName","start","end","getSequence","getRefNames","opts","setup","getSequenceNames","getRegions","seqSizes","getSequenceSizes","Object","keys","map","getHeader","loc","uri","readFile","setupP","catch","e","undefined","getFeatures","region","ObservableCreate","size","getSequenceSize","regionEnd","Math","min","chunks","chunkSize","s","chunkStart","r","push","get","JSON","stringify","seq","Promise","all","join","slice","observer","next","SimpleFeature","id","data","complete","freeResources"],"sourceRoot":""}
\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/static/js/9245.d882c265.chunk.js
--- a/x/static/js/9245.d882c265.chunk.js Fri Oct 18 11:57:55 2024 +0000
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d=g.map((e=>e.toLowerCase()));class w{constructor({filehandle:e,path:t}){if(e)this.filehandle=e;else{if(!t)throw new Error("must supply path or filehandle");this.filehandle=new c.EY(t)}}async _detectEndianness(){const e=await this.filehandle.read(l.hp.allocUnsafe(8),0,8,0),{buffer:t}=e;if(t.readInt32LE(0)!==f)throw t.readInt32BE(0)===f?new Error("big endian not supported"):new Error("not a 2bit file");this.version=t.readInt32LE(4)}async getHeader(){await this._detectEndianness();const{buffer:e}=await this.filehandle.read(l.hp.allocUnsafe(16),0,16,0),t=e,n=!0,s=new DataView(t.buffer,t.byteOffset,t.length);let i=0;const a=s.getInt32(i,n);if(i+=4,440477507!==a)throw new Error(`Wrong magic number ${a}`);const r=s.getInt32(i,n);i+=4;const o=s.getUint32(i,n);return i+=4,{version:r,magic:a,sequenceCount:o,reserved:s.getUint32(i,n)}}async getIndex(){const e=await this.getHeader(),t=8+e.sequenceCount*(257+(1===this.version?8:4)),{buffer:n}=await 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e=r.getUint32(a,i);a+=4,f.push(e)}return{maskBlockCount:o,maskBlockSizes:f,maskBlockStarts:c,reserved:r.getInt32(a,i)}}async _getSequenceRecord(e){const t=await this._record1(e),n=8*t.nBlockCount+8,s=await this._record2(e+4,n),i=8*s.maskBlockCount+8,a=await this._record3(e+4+n-4,i);return{dnaSize:t.dnaSize,nBlocks:{starts:s.nBlockStarts,sizes:s.nBlockSizes},maskBlocks:{starts:a.maskBlockStarts,sizes:a.maskBlockSizes},dnaPosition:e+4+n-4+i}}async getSequence(e,t=0,n=Number.POSITIVE_INFINITY){const s=(await this.getIndex())[e];if(!s)return;const i=await this._getSequenceRecord(s);if(t<0)throw new TypeError("regionStart cannot be less than 0");(void 0===n||n>i.dnaSize)&&(n=i.dnaSize);const a=this._getOverlappingBlocks(t,n,i.nBlocks.starts,i.nBlocks.sizes),r=this._getOverlappingBlocks(t,n,i.maskBlocks.starts,i.maskBlocks.sizes),o=l.hp.allocUnsafe(Math.ceil((n-t)/4)+1),c=Math.floor(t/4),{buffer:f}=await this.filehandle.read(o,0,o.length,i.dnaPosition+c);let h="";for(let 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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9280.6e897b98.chunk.js.map
--- a/x/static/js/9280.6e897b98.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9292.96b77fb0.chunk.js
--- a/x/static/js/9292.96b77fb0.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9305.4d748fb5.chunk.js
--- a/x/static/js/9305.4d748fb5.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9305.4d748fb5.chunk.js.map
--- a/x/static/js/9305.4d748fb5.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9314.3e43d34c.chunk.js
--- a/x/static/js/9314.3e43d34c.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9329.c269472b.chunk.js
--- a/x/static/js/9329.c269472b.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/937.4f610bdf.chunk.js
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/937.4f610bdf.chunk.js.map
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9372.67d6f914.chunk.js
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9372.67d6f914.chunk.js.map
--- a/x/static/js/9372.67d6f914.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9374.8ac7e6d7.chunk.js
--- a/x/static/js/9374.8ac7e6d7.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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-"use strict";(globalThis.webpackChunk_jbrowse_web=globalThis.webpackChunk_jbrowse_web||[]).push([[9374],{39374:(e,l,t)=>{t.r(l),t.d(l,{default:()=>m});var n=t(7552),r=t(29499),a=t(24387),c=t(58507),o=t(5401),i=t(49823);function m({handleClose:e}){return n.createElement(i.Dialog,{open:!0,maxWidth:"xl",onClose:e,title:"Using the search box"},n.createElement(r.A,null,n.createElement("h3",null,"Searching"),n.createElement("ul",null,n.createElement("li",null,"Jump to a feature or reference sequence by typing its name in the location box and pressing Enter."),n.createElement("li",null,"Jump to a specific region by typing the region into the location box as: ",n.createElement("code",null,"ref:start..end")," or ",n.createElement("code",null,"ref:start-end"),". Commas are allowed in the start and end coordinates. A space-separated list of locstrings can be used to open up multiple chromosomes at a time")),n.createElement("h3",null,"Example Searches"),n.createElement("ul",null,n.createElement("li",null,n.createElement("code",null,"BRCA")," - searches for the feature named BRCA"),n.createElement("li",null,n.createElement("code",null,"chr4")," - jumps to chromosome 4"),n.createElement("li",null,n.createElement("code",null,"chr4:79,500,000..80,000,000")," - jumps the region on chromosome 4 between 79.5Mb and 80Mb."),n.createElement("li",null,n.createElement("code",null,"chr1:1-100 chr2:1-100")," - create a split view of chr1:1-100 and chr2:1-100"),n.createElement("li",null,n.createElement("code",null,"chr1 chr2 chr3")," - open up multiple chromosomes at once"),n.createElement("li",null,n.createElement("code",null,"chr1:1-100[rev] chr2:1-100")," - open up the first region in the horizontally flipped orientation"),n.createElement("li",null,n.createElement("code",null,"chr1 100 200")," - use whitespace separated refname, start, end"))),n.createElement(a.A,null),n.createElement(c.A,null,n.createElement(o.A,{onClick:()=>{e()},color:"primary"},"Close")))}}}]);
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9374.8ac7e6d7.chunk.js.map
--- a/x/static/js/9374.8ac7e6d7.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/static/js/9384.a4e7a69a.chunk.js
--- a/x/static/js/9384.a4e7a69a.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9409.c7569196.chunk.js.map
--- a/x/static/js/9409.c7569196.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9449.2e1d2652.chunk.js
--- a/x/static/js/9449.2e1d2652.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9449.2e1d2652.chunk.js.map
--- a/x/static/js/9449.2e1d2652.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9458.07f0ae54.chunk.js
--- a/x/static/js/9458.07f0ae54.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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internal component.\\n */\\nimport { jsx as _jsx } from \\"react/jsx-runtime\\";\\nexport default createSvgIcon(/*#__PURE__*/_jsx(\\"path\\", {\\n d: \\"M19 13h-6v6h-2v-6H5v-2h6V5h2v6h6v2z\\"\\n}), \'Add\');","import generateUtilityClasses from \'@mui/utils/generateUtilityClasses\';\\nimport generateUtilityClass from \'@mui/utils/generateUtilityClass\';\\nexport function getSpeedDialIconUtilityClass(slot) {\\n return generateUtilityClass(\'MuiSpeedDialIcon\', slot);\\n}\\nconst speedDialIconClasses = generateUtilityClasses(\'MuiSpeedDialIcon\', [\'root\', \'icon\', \'iconOpen\', \'iconWithOpenIconOpen\', \'openIcon\', \'openIconOpen\']);\\nexport default speedDialIconClasses;","\'use client\';\\n\\nimport * as React from \'react\';\\nimport PropTypes from \'prop-types\';\\nimport clsx from \'clsx\';\\nimport composeClasses from \'@mui/utils/composeClasses\';\\nimport { styled } from \\"../zero-styled/index.js\\";\\nimport memoTheme from \\"../utils/memoTheme.js\\";\\nimport { useDefaultProps } from \\"../DefaultPropsProvider/index.js\\";\\nimport AddIcon from \\"../internal/svg-icons/Add.js\\";\\nimport speedDialIconClasses, { getSpeedDialIconUtilityClass } from \\"./speedDialIconClasses.js\\";\\nimport { jsx as _jsx, jsxs as _jsxs } from \\"react/jsx-runtime\\";\\nconst useUtilityClasses = ownerState => {\\n const {\\n classes,\\n open,\\n openIcon\\n } = ownerState;\\n const slots = {\\n root: [\'root\'],\\n icon: [\'icon\', open && \'iconOpen\', openIcon && open && \'iconWithOpenIconOpen\'],\\n openIcon: [\'openIcon\', open && \'openIconOpen\']\\n };\\n return composeClasses(slots, getSpeedDialIconUtilityClass, classes);\\n};\\nconst SpeedDialIconRoot = styled(\'span\', {\\n name: \'Mui'..b'.short\\n })\\n },\\n [`& .${speedDialIconClasses.openIcon}`]: {\\n position: \'absolute\',\\n transition: theme.transitions.create([\'transform\', \'opacity\'], {\\n duration: theme.transitions.duration.short\\n }),\\n opacity: 0,\\n transform: \'rotate(-45deg)\'\\n },\\n variants: [{\\n props: ({\\n ownerState\\n }) => ownerState.open,\\n style: {\\n [`& .${speedDialIconClasses.icon}`]: {\\n transform: \'rotate(45deg)\'\\n }\\n }\\n }, {\\n props: ({\\n ownerState\\n }) => ownerState.open && ownerState.openIcon,\\n style: {\\n [`& .${speedDialIconClasses.icon}`]: {\\n opacity: 0\\n }\\n }\\n }, {\\n props: ({\\n ownerState\\n }) => ownerState.open,\\n style: {\\n [`& .${speedDialIconClasses.openIcon}`]: {\\n transform: \'rotate(0deg)\',\\n opacity: 1\\n }\\n }\\n }]\\n})));\\nconst SpeedDialIcon = /*#__PURE__*/React.forwardRef(function SpeedDialIcon(inProps, ref) {\\n const props = useDefaultProps({\\n props: inProps,\\n name: \'MuiSpeedDialIcon\'\\n });\\n const {\\n className,\\n icon: iconProp,\\n open,\\n openIcon: openIconProp,\\n ...other\\n } = props;\\n const ownerState = props;\\n const classes = useUtilityClasses(ownerState);\\n function formatIcon(icon, newClassName) {\\n if (/*#__PURE__*/React.isValidElement(icon)) {\\n return /*#__PURE__*/React.cloneElement(icon, {\\n className: newClassName\\n });\\n }\\n return icon;\\n }\\n return /*#__PURE__*/_jsxs(SpeedDialIconRoot, {\\n className: clsx(classes.root, className),\\n ref: ref,\\n ownerState: ownerState,\\n ...other,\\n children: [openIconProp ? formatIcon(openIconProp, classes.openIcon) : null, iconProp ? formatIcon(iconProp, classes.icon) : /*#__PURE__*/_jsx(AddIcon, {\\n className: classes.icon\\n })]\\n });\\n});\\nprocess.env.NODE_ENV !== \\"production\\" ? SpeedDialIcon.propTypes /* remove-proptypes */ = {\\n // \xe2\x94\x8c\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80 Warning \xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x90\\n // \xe2\x94\x82 These PropTypes are generated from the TypeScript type definitions. \xe2\x94\x82\\n // \xe2\x94\x82 To update them, edit the d.ts file and run `pnpm proptypes`. \xe2\x94\x82\\n // \xe2\x94\x94\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x80\xe2\x94\x98\\n /**\\n * Override or extend the styles applied to the component.\\n */\\n classes: PropTypes.object,\\n /**\\n * @ignore\\n */\\n className: PropTypes.string,\\n /**\\n * The icon to display.\\n */\\n icon: PropTypes.node,\\n /**\\n * @ignore\\n * If `true`, the component is shown.\\n */\\n open: PropTypes.bool,\\n /**\\n * The icon to display in the SpeedDial Floating Action Button when the SpeedDial is open.\\n */\\n openIcon: PropTypes.node,\\n /**\\n * The system prop that allows defining system overrides as well as additional CSS styles.\\n */\\n sx: PropTypes.oneOfType([PropTypes.arrayOf(PropTypes.oneOfType([PropTypes.func, PropTypes.object, PropTypes.bool])), PropTypes.func, PropTypes.object])\\n} : void 0;\\nSpeedDialIcon.muiName = \'SpeedDialIcon\';\\nexport default SpeedDialIcon;"],"names":["createSvgIcon","d","getSpeedDialIconUtilityClass","slot","generateUtilityClass","generateUtilityClasses","SpeedDialIconRoot","styled","name","overridesResolver","props","styles","ownerState","icon","open","iconOpen","openIcon","iconWithOpenIconOpen","openIconOpen","root","memoTheme","theme","height","transition","transitions","create","duration","short","position","opacity","transform","variants","style","SpeedDialIcon","inProps","ref","className","iconProp","openIconProp","other","classes","slots","composeClasses","useUtilityClasses","formatIcon","newClassName","clsx","children","Add","muiName"],"sourceRoot":""}\n\\ No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/946.245d7df9.chunk.js
--- a/x/static/js/946.245d7df9.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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--- a/x/static/js/946.245d7df9.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9589.9087e0ea.chunk.js
--- a/x/static/js/9589.9087e0ea.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,2 +0,0 @@
-"use strict";(globalThis.webpackChunk_jbrowse_web=globalThis.webpackChunk_jbrowse_web||[]).push([[9589],{49589:(e,t,a)=>{a.r(t),a.d(t,{default:()=>m});var o=a(7552),l=a(68446),n=a(29499),r=a(36715),c=a(1343),s=a(58507),i=a(5401),h=a(49823);const u=(0,a(75785).n9)()({root:{width:500}}),m=(0,l.observer)((function(e){const{model:t,handleClose:a}=e,{classes:l}=u(),{maxHeight:m=""}=t,[b,d]=(0,o.useState)(`${m}`);return o.createElement(h.Dialog,{open:!0,onClose:a,title:"Set max height"},o.createElement(n.A,{className:l.root},o.createElement(r.A,null,'Set max height for the track. For example, you can increase this if the layout says "Max height reached"'),o.createElement(c.A,{value:b,autoFocus:!0,onChange:e=>{d(e.target.value)},placeholder:"Enter max height for layout"}),o.createElement(s.A,null,o.createElement(i.A,{variant:"contained",color:"primary",type:"submit",autoFocus:!0,onClick:()=>{t.setMaxHeight(""===b||Number.isNaN(+b)?void 0:+b),a()}},"Submit"),o.createElement(i.A,{variant:"contained",color:"secondary",onClick:()=>{a()}},"Cancel"))))}))}}]);
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9589.9087e0ea.chunk.js.map
--- a/x/static/js/9589.9087e0ea.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
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\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/static/js/965.8524fdac.chunk.js
--- a/x/static/js/965.8524fdac.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,2 +0,0 @@
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/965.8524fdac.chunk.js.map
--- a/x/static/js/965.8524fdac.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9657.0cccd5bf.chunk.js
--- a/x/static/js/9657.0cccd5bf.chunk.js Fri Oct 18 11:57:55 2024 +0000
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--- a/x/static/js/9658.33669a59.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9675.b4f16970.chunk.js
--- a/x/static/js/9675.b4f16970.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9675.b4f16970.chunk.js.map
--- a/x/static/js/9675.b4f16970.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9756.4ac80c37.chunk.js
--- a/x/static/js/9756.4ac80c37.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9756.4ac80c37.chunk.js.map
--- a/x/static/js/9756.4ac80c37.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9824.b9ece376.chunk.js
--- a/x/static/js/9824.b9ece376.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9824.b9ece376.chunk.js.map
--- a/x/static/js/9824.b9ece376.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
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-{"version":3,"file":"static/js/9824.b9ece376.chunk.js","mappings":"0IASA,Q,QAJsC,e,oMCH/B,SAASA,EAA2BC,GACzC,OAAO,EAAAC,EAAA,IAAqB,iBAAkBD,EAChD,CACA,MACA,GAD2B,EAAAE,EAAA,GAAuB,iBAAkB,CAAC,S,eCMrE,MASMC,GAAkB,EAAAC,EAAA,IAAO,QAAS,CACtCC,KAAM,iBACNL,KAAM,OACNM,kBAAmB,CAACC,EAAOC,IAAWA,EAAOC,MAHvB,CAIrB,CACDC,QAAS,uBAELC,EAAY,CAChBC,QAAS,UAELC,EAAmB,QAuDzB,EAtDiC,cAAiB,SAAqBC,EAASC,GAC9E,MAAMR,GAAQ,OAAgB,CAC5BA,MAAOO,EACPT,KAAM,oBAEF,UACJW,EAAS,UACTC,EAAYJ,KACTK,GACDX,EACEY,EAAa,IACdZ,EACHU,aAEIG,EAlCkBD,KACxB,MAAM,QACJC,GACED,EAIJ,OAAO,EAAAE,EAAA,GAHO,CACZZ,KAAM,CAAC,SAEoBV,EAA4BqB,EAAQ,EA2BjDE,CAAkBH,GAClC,OAAoB,SAAKI,EAAA,EAAiBC,SAAU,CAClDC,MAAOd,EACPe,UAAuB,SAAKvB,EAAiB,CAC3CwB,GAAIV,EACJD,WAAW,EAAAY,EAAA,GAAKR,EAAQX,KAAMO,GAC9BD,IAAKA,EACLc,KAAMZ,IAAcJ,EAAmB,KAAO,WAC9CM,WAAYA,KACTD,KAGT,G","sources":["../../../node_modules/@mui/material/Table/Tablelvl2Context.js","../../../node_modules/@mui/material/TableFooter/tableFooterClasses.js","../../../node_modules/@mui/material/TableFooter/TableFooter.js"],"sourcesContent":["import * as React from 'react';\n\n/**\n * @ignore - internal component.\n */\nconst Tablelvl2Context = /*#__PURE__*/React.createContext();\nif (process.env.NODE_ENV !== 'production') {\n Tablelvl2Context.displayName = 'Tablelvl2Context';\n}\nexport default Tablelvl2Context;","import generateUtilityClasses from '@mui/utils/generateUtilityClasses';\nimport generateUtilityClass from '@mui/utils/generateUtilityClass';\nexport function getTableFooterUtilityClass(slot) {\n return generateUtilityClass('MuiTableFooter', slot);\n}\nconst tableFooterClasses = generateUtilityClasses('MuiTableFooter', ['root']);\nexport default tableFooterClasses;","'use client';\n\nimport * as React from 'react';\nimport PropTypes from 'prop-types';\nimport clsx from 'clsx';\nimport composeClasses from '@mui/utils/composeClasses';\nimport Tablelvl2Context from \"../Table/Tablelvl2Context.js\";\nimport { styled } from \"../zero-styled/index.js\";\nimport { useDefaultProps } from \"../DefaultPropsProvider/index.js\";\nimport { getTableFooterUtilityClass } from \"./tableFooterClasses.js\";\nimport { jsx as _jsx } from \"react/jsx-runtime\";\nconst useUtilityClasses = ownerState => {\n const {\n classes\n } = ownerState;\n const slots = {\n root: ['root']\n };\n return composeClasses(slots, getTableFooterUtilityClass, classes);\n};\nconst TableFooterRoot = styled('tfoot', {\n name: 'MuiTableFooter',\n slot: 'Root',\n overridesResolver: (props, styles) => styles.root\n})({\n display: 'table-footer-group'\n});\nconst tablelvl2 = {\n variant: 'footer'\n};\nconst defaultComponent = 'tfoot';\nconst TableFooter = /*#__PURE__*/React.forwardRef(function TableFooter(inProps, ref) {\n const props = useDefaultProps({\n props: inProps,\n name: 'MuiTableFooter'\n });\n const {\n className,\n component = defaultComponent,\n ...other\n } = props;\n const ownerState = {\n ...props,\n component\n };\n const classes = useUtilityClasses(ownerState);\n return /*#__PURE__*/_jsx(Tablelvl2Context.Provider, {\n value: tablelvl2,\n children: /*#__PURE__*/_jsx(TableFooterRoot, {\n as: component,\n className: clsx(classes.root, className),\n ref: ref,\n role: component === defaultComponent ? null : 'rowgroup',\n ownerState: ownerState,\n ...other\n })\n });\n});\nprocess.env.NODE_ENV !== \"production\" ? TableFooter.propTypes /* remove-proptypes */ = {\n // ┌────────────────────────────── Warning ──────────────────────────────┐\n // │ These PropTypes are generated from the TypeScript type definitions. │\n // │ To update them, edit the d.ts file and run `pnpm proptypes`. │\n // └─────────────────────────────────────────────────────────────────────┘\n /**\n * The content of the component, normally `TableRow`.\n */\n children: PropTypes.node,\n /**\n * Override or extend the styles applied to the component.\n */\n classes: PropTypes.object,\n /**\n * @ignore\n */\n className: PropTypes.string,\n /**\n * The component used for the root node.\n * Either a string to use a HTML element or a component.\n */\n component: PropTypes.elementType,\n /**\n * The system prop that allows defining system overrides as well as additional CSS styles.\n */\n sx: PropTypes.oneOfType([PropTypes.arrayOf(PropTypes.oneOfType([PropTypes.func, PropTypes.object, PropTypes.bool])), PropTypes.func, PropTypes.object])\n} : void 0;\nexport default TableFooter;"],"names":["getTableFooterUtilityClass","slot","generateUtilityClass","generateUtilityClasses","TableFooterRoot","styled","name","overridesResolver","props","styles","root","display","tablelvl2","variant","defaultComponent","inProps","ref","className","component","other","ownerState","classes","composeClasses","useUtilityClasses","Tablelvl2Context","Provider","value","children","as","clsx","role"],"sourceRoot":""}
\ No newline at end of file

diff -r cec274db51c0 -r ed3a21033188 x/static/js/9831.de8b3aa9.chunk.js
--- a/x/static/js/9831.de8b3aa9.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,2 +0,0 @@\n-(globalThis.webpackChunk_jbrowse_web=globalThis.webpackChunk_jbrowse_web||[]).push([[9831],{29831:function(e,t,r){var i;e.exports=(i=r(17753),r(29038),r(1224),r(59982),r(47089),function(){var e=i,t=e.lib.BlockCipher,r=e.algo,n=[],s=[],o=[],c=[],a=[],h=[],f=[],u=[],d=[],l=[];!function(){for(var e=[],t=0;t<256;t++)e[t]=t<128?t<<1:t<<1^283;var r=0,i=0;for(t=0;t<256;t++){var p=i^i<<1^i<<2^i<<3^i<<4;p=p>>>8^255&p^99,n[r]=p,s[p]=r;var _=e[r],v=e[_],y=e[v],g=257*e[p]^16843008*p;o[r]=g<<24|g>>>8,c[r]=g<<16|g>>>16,a[r]=g<<8|g>>>24,h[r]=g,g=16843009*y^65537*v^257*_^16843008*r,f[p]=g<<24|g>>>8,u[p]=g<<16|g>>>16,d[p]=g<<8|g>>>24,l[p]=g,r?(r=_^e[e[e[y^_]]],i^=e[e[i]]):r=i=1}}();var p=[0,1,2,4,8,16,32,64,128,27,54],_=r.AES=t.extend({_doReset:function(){if(!this._nRounds||this._keyPriorReset!==this._key){for(var e=this._keyPriorReset=this._key,t=e.words,r=e.sigBytes/4,i=4*((this._nRounds=r+6)+1),s=this._keySchedule=[],o=0;o<i;o++)o<r?s[o]=t[o]:(h=s[o-1],o%r?r>6&&o%r==4&&(h=n[h>>>24]<<24|n[h>>>16&255]<<16|n[h>>>8&255]<<8|n[255&h]):(h=n[(h=h<<8|h>>>24)>>>24]<<24|n[h>>>16&255]<<16|n[h>>>8&255]<<8|n[255&h],h^=p[o/r|0]<<24),s[o]=s[o-r]^h);for(var c=this._invKeySchedule=[],a=0;a<i;a++){if(o=i-a,a%4)var h=s[o];else h=s[o-4];c[a]=a<4||o<=4?h:f[n[h>>>24]]^u[n[h>>>16&255]]^d[n[h>>>8&255]]^l[n[255&h]]}}},encryptBlock:function(e,t){this._doCryptBlock(e,t,this._keySchedule,o,c,a,h,n)},decryptBlock:function(e,t){var r=e[t+1];e[t+1]=e[t+3],e[t+3]=r,this._doCryptBlock(e,t,this._invKeySchedule,f,u,d,l,s),r=e[t+1],e[t+1]=e[t+3],e[t+3]=r},_doCryptBlock:function(e,t,r,i,n,s,o,c){for(var a=this._nRounds,h=e[t]^r[0],f=e[t+1]^r[1],u=e[t+2]^r[2],d=e[t+3]^r[3],l=4,p=1;p<a;p++){var _=i[h>>>24]^n[f>>>16&255]^s[u>>>8&255]^o[255&d]^r[l++],v=i[f>>>24]^n[u>>>16&255]^s[d>>>8&255]^o[255&h]^r[l++],y=i[u>>>24]^n[d>>>16&255]^s[h>>>8&255]^o[255&f]^r[l++],g=i[d>>>24]^n[h>>>16&255]^s[f>>>8&255]^o[255&u]^r[l++];h=_,f=v,u=y,d=g}_=(c[h>>>24]<<24|c[f>>>16&255]<<16|c[u>>>8&255]<<8|c[255&d])^r[l++],v=(c[f>>>24]<<24|c[u>>>16&255]<<16|c[d>>>8&255]<<8|c[255&h])^r[l++],y=(c[u>>>24]<<24|c[d>>>16&255]<<16|c[h>>>8&255]<<8|c[255&f])^r[l++],g=(c[d>>>24]<<24|c[h>>>16&255]<<16|c[f>>>8&255]<<8|c[255&u])^r[l++],e[t]=_,e[t+1]=v,e[t+2]=y,e[t+3]=g},keySize:8});e.AES=t._createHelper(_)}(),i.AES)},47089:function(e,t,r){var i,n,s,o,c,a,h,f,u,d,l,p,_,v,y,g,k,B,x;e.exports=(i=r(17753),r(59982),void(i.lib.Cipher||(n=i,s=n.lib,o=s.Base,c=s.WordArray,a=s.BufferedBlockAlgorithm,h=n.enc,h.Utf8,f=h.Base64,u=n.algo.EvpKDF,d=s.Cipher=a.extend({cfg:o.extend(),createEncryptor:function(e,t){return this.create(this._ENC_XFORM_MODE,e,t)},createDecryptor:function(e,t){return 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0):i=this._prevBlock;for(var s=0;s<r;s++)e[t+s]^=i[s]}return e.Encryptor=e.extend({processBlock:function(e,r){var i=this._cipher,n=i.blockSize;t.call(this,e,r,n),i.encryptBlock(e,r),this._prevBlock=e.slice(r,r+n)}}),e.Decryptor=e.extend({processBlock:function(e,r){var i=this._cipher,n=i.blockSize,s=e.slice(r,r+n);i.decryptBlock(e,r),t.call(this,e,r,n),this._prevBlock=s}}),e}'..b'.sin(t+1))|0}();var a=o.MD5=s.extend({_doReset:function(){this._hash=new n.init([1732584193,4023233417,2562383102,271733878])},_doProcessBlock:function(e,t){for(var r=0;r<16;r++){var i=t+r,n=e[i];e[i]=16711935&(n<<8|n>>>24)|4278255360&(n<<24|n>>>8)}var s=this._hash.words,o=e[t+0],a=e[t+1],l=e[t+2],p=e[t+3],_=e[t+4],v=e[t+5],y=e[t+6],g=e[t+7],k=e[t+8],B=e[t+9],x=e[t+10],m=e[t+11],S=e[t+12],z=e[t+13],b=e[t+14],C=e[t+15],M=s[0],w=s[1],D=s[2],E=s[3];M=h(M,w,D,E,o,7,c[0]),E=h(E,M,w,D,a,12,c[1]),D=h(D,E,M,w,l,17,c[2]),w=h(w,D,E,M,p,22,c[3]),M=h(M,w,D,E,_,7,c[4]),E=h(E,M,w,D,v,12,c[5]),D=h(D,E,M,w,y,17,c[6]),w=h(w,D,E,M,g,22,c[7]),M=h(M,w,D,E,k,7,c[8]),E=h(E,M,w,D,B,12,c[9]),D=h(D,E,M,w,x,17,c[10]),w=h(w,D,E,M,m,22,c[11]),M=h(M,w,D,E,S,7,c[12]),E=h(E,M,w,D,z,12,c[13]),D=h(D,E,M,w,b,17,c[14]),M=f(M,w=h(w,D,E,M,C,22,c[15]),D,E,a,5,c[16]),E=f(E,M,w,D,y,9,c[17]),D=f(D,E,M,w,m,14,c[18]),w=f(w,D,E,M,o,20,c[19]),M=f(M,w,D,E,v,5,c[20]),E=f(E,M,w,D,x,9,c[21]),D=f(D,E,M,w,C,14,c[22]),w=f(w,D,E,M,_,20,c[23]),M=f(M,w,D,E,B,5,c[24]),E=f(E,M,w,D,b,9,c[25]),D=f(D,E,M,w,p,14,c[26]),w=f(w,D,E,M,k,20,c[27]),M=f(M,w,D,E,z,5,c[28]),E=f(E,M,w,D,l,9,c[29]),D=f(D,E,M,w,g,14,c[30]),M=u(M,w=f(w,D,E,M,S,20,c[31]),D,E,v,4,c[32]),E=u(E,M,w,D,k,11,c[33]),D=u(D,E,M,w,m,16,c[34]),w=u(w,D,E,M,b,23,c[35]),M=u(M,w,D,E,a,4,c[36]),E=u(E,M,w,D,_,11,c[37]),D=u(D,E,M,w,g,16,c[38]),w=u(w,D,E,M,x,23,c[39]),M=u(M,w,D,E,z,4,c[40]),E=u(E,M,w,D,o,11,c[41]),D=u(D,E,M,w,p,16,c[42]),w=u(w,D,E,M,y,23,c[43]),M=u(M,w,D,E,B,4,c[44]),E=u(E,M,w,D,S,11,c[45]),D=u(D,E,M,w,C,16,c[46]),M=d(M,w=u(w,D,E,M,l,23,c[47]),D,E,o,6,c[48]),E=d(E,M,w,D,g,10,c[49]),D=d(D,E,M,w,b,15,c[50]),w=d(w,D,E,M,v,21,c[51]),M=d(M,w,D,E,S,6,c[52]),E=d(E,M,w,D,p,10,c[53]),D=d(D,E,M,w,x,15,c[54]),w=d(w,D,E,M,a,21,c[55]),M=d(M,w,D,E,k,6,c[56]),E=d(E,M,w,D,C,10,c[57]),D=d(D,E,M,w,y,15,c[58]),w=d(w,D,E,M,z,21,c[59]),M=d(M,w,D,E,_,6,c[60]),E=d(E,M,w,D,m,10,c[61]),D=d(D,E,M,w,l,15,c[62]),w=d(w,D,E,M,B,21,c[63]),s[0]=s[0]+M|0,s[1]=s[1]+w|0,s[2]=s[2]+D|0,s[3]=s[3]+E|0},_doFinalize:function(){var t=this._data,r=t.words,i=8*this._nDataBytes,n=8*t.sigBytes;r[n>>>5]|=128<<24-n%32;var s=e.floor(i/4294967296),o=i;r[15+(n+64>>>9<<4)]=16711935&(s<<8|s>>>24)|4278255360&(s<<24|s>>>8),r[14+(n+64>>>9<<4)]=16711935&(o<<8|o>>>24)|4278255360&(o<<24|o>>>8),t.sigBytes=4*(r.length+1),this._process();for(var c=this._hash,a=c.words,h=0;h<4;h++){var f=a[h];a[h]=16711935&(f<<8|f>>>24)|4278255360&(f<<24|f>>>8)}return c},clone:function(){var e=s.clone.call(this);return e._hash=this._hash.clone(),e}});function h(e,t,r,i,n,s,o){var c=e+(t&r|~t&i)+n+o;return(c<<s|c>>>32-s)+t}function f(e,t,r,i,n,s,o){var c=e+(t&i|r&~i)+n+o;return(c<<s|c>>>32-s)+t}function u(e,t,r,i,n,s,o){var c=e+(t^r^i)+n+o;return(c<<s|c>>>32-s)+t}function d(e,t,r,i,n,s,o){var c=e+(r^(t|~i))+n+o;return(c<<s|c>>>32-s)+t}t.MD5=s._createHelper(a),t.HmacMD5=s._createHmacHelper(a)}(Math),i.MD5)},62555:function(e,t,r){var i,n,s,o,c,a,h,f;e.exports=(n=(i=f=r(17753)).lib,s=n.WordArray,o=n.Hasher,c=i.algo,a=[],h=c.SHA1=o.extend({_doReset:function(){this._hash=new s.init([1732584193,4023233417,2562383102,271733878,3285377520])},_doProcessBlock:function(e,t){for(var r=this._hash.words,i=r[0],n=r[1],s=r[2],o=r[3],c=r[4],h=0;h<80;h++){if(h<16)a[h]=0|e[t+h];else{var f=a[h-3]^a[h-8]^a[h-14]^a[h-16];a[h]=f<<1|f>>>31}var u=(i<<5|i>>>27)+c+a[h];u+=h<20?1518500249+(n&s|~n&o):h<40?1859775393+(n^s^o):h<60?(n&s|n&o|s&o)-1894007588:(n^s^o)-899497514,c=o,o=s,s=n<<30|n>>>2,n=i,i=u}r[0]=r[0]+i|0,r[1]=r[1]+n|0,r[2]=r[2]+s|0,r[3]=r[3]+o|0,r[4]=r[4]+c|0},_doFinalize:function(){var e=this._data,t=e.words,r=8*this._nDataBytes,i=8*e.sigBytes;return t[i>>>5]|=128<<24-i%32,t[14+(i+64>>>9<<4)]=Math.floor(r/4294967296),t[15+(i+64>>>9<<4)]=r,e.sigBytes=4*t.length,this._process(),this._hash},clone:function(){var e=o.clone.call(this);return e._hash=this._hash.clone(),e}}),i.SHA1=o._createHelper(h),i.HmacSHA1=o._createHmacHelper(h),f.SHA1)}}]);\n-//# sourceMappingURL=9831.de8b3aa9.chunk.js.map\n\\ No newline at end of file\n'

diff -r cec274db51c0 -r ed3a21033188 x/static/js/9831.de8b3aa9.chunk.js.map
--- a/x/static/js/9831.de8b3aa9.chunk.js.map Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9870.f395e633.chunk.js
--- a/x/static/js/9870.f395e633.chunk.js Fri Oct 18 11:57:55 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9870.f395e633.chunk.js.map
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/9943.d3ab0f18.chunk.js
--- a/x/static/js/9943.d3ab0f18.chunk.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/main.1532dd54.js
--- a/x/static/js/main.1532dd54.js Fri Oct 18 11:57:55 2024 +0000
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diff -r cec274db51c0 -r ed3a21033188 x/static/js/main.1532dd54.js.LICENSE.txt
--- a/x/static/js/main.1532dd54.js.LICENSE.txt Fri Oct 18 11:57:55 2024 +0000
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