| Next changeset 1:b79f6002b176 (2020-11-10) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit 1db2b3ee758847b8b63f58fb2075961003ff8c22" |
|
added:
images/maf_icons/interval2maf.png interval2maf.py interval2maf.xml macros.xml test-data/interval2maf-in1.bed test-data/interval2maf-in1.maf test-data/interval2maf-in1.maf.index test-data/interval2maf-in2.bed test-data/interval2maf-in3.bed test-data/interval2maf-out1.maf test-data/interval2maf-out2.maf test-data/interval2maf-out3.maf test-data/local/interval2maf-in1-1.maf test-data/local/interval2maf-in1-1.maf.index test-data/local/interval2maf-in1-2.maf test-data/local/interval2maf-in1-2.maf.index test-data/local/maf_indexes.loc tool-data/maf_indexes.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| b |
| diff -r 000000000000 -r cfea1d6354db images/maf_icons/interval2maf.png |
| b |
| Binary file images/maf_icons/interval2maf.png has changed |
| b |
| diff -r 000000000000 -r cfea1d6354db interval2maf.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/interval2maf.py Fri Jul 17 10:56:42 2020 -0400 |
| [ |
| @@ -0,0 +1,145 @@ +#!/usr/bin/env python +""" +Reads a list of intervals and a maf. Produces a new maf containing the +blocks or parts of blocks in the original that overlapped the intervals. + +If a MAF file, not UID, is provided the MAF file is indexed before being processed. + +NOTE: If two intervals overlap the same block it will be written twice. + +usage: %prog maf_file [options] + -d, --dbkey=d: Database key, ie hg17 + -c, --chromCol=c: Column of Chr + -s, --startCol=s: Column of Start + -e, --endCol=e: Column of End + -S, --strandCol=S: Column of Strand + -t, --mafType=t: Type of MAF source to use + -m, --mafFile=m: Path of source MAF file, if not using cached version + -s, --mafFiles=s: Path of source MAF files, if using cached version + -I, --mafIndex=I: Path of precomputed source MAF file index, if not using cached version + -i, --interval_file=i: Input interval file + -o, --output_file=o: Output MAF file + -p, --species=p: Species to include in output + -P, --split_blocks_by_species=P: Split blocks by species + -r, --remove_all_gap_columns=r: Remove all Gap columns + -l, --indexLocation=l: Override default maf_index.loc file + -z, --mafIndexFile=z: Directory of local maf index file ( maf_index.loc or maf_pairwise.loc ) +""" +# Dan Blankenberg +from __future__ import print_function + +import bx.align.maf +import bx.intervals.io +from bx.cookbook import doc_optparse +from galaxy.tools.util import maf_utilities + + +def __main__(): + index = index_filename = None + + # Parse Command Line + options, args = doc_optparse.parse(__doc__) + + if options.dbkey: + dbkey = options.dbkey + else: + dbkey = None + if dbkey in [None, "?"]: + maf_utilities.tool_fail("You must specify a proper build in order to extract alignments. You can specify your genome build by clicking on the pencil icon associated with your interval file.") + + species = maf_utilities.parse_species_option(options.species) + + if options.chromCol: + chromCol = int(options.chromCol) - 1 + else: + maf_utilities.tool_fail("Chromosome column not set, click the pencil icon in the history item to set the metadata attributes.") + + if options.startCol: + startCol = int(options.startCol) - 1 + else: + maf_utilities.tool_fail("Start column not set, click the pencil icon in the history item to set the metadata attributes.") + + if options.endCol: + endCol = int(options.endCol) - 1 + else: + maf_utilities.tool_fail("End column not set, click the pencil icon in the history item to set the metadata attributes.") + + if options.strandCol: + strandCol = int(options.strandCol) - 1 + else: + strandCol = -1 + + if options.interval_file: + interval_file = options.interval_file + else: + maf_utilities.tool_fail("Input interval file has not been specified.") + + if options.output_file: + output_file = options.output_file + else: + maf_utilities.tool_fail("Output file has not been specified.") + + split_blocks_by_species = remove_all_gap_columns = False + if options.split_blocks_by_species and options.split_blocks_by_species == 'split_blocks_by_species': + split_blocks_by_species = True + if options.remove_all_gap_columns and options.remove_all_gap_columns == 'remove_all_gap_columns': + remove_all_gap_columns = True + else: + remove_all_gap_columns = True + # Finish parsing command line + + # Open indexed access to MAFs + if options.mafType: + if options.indexLocation: + index = maf_utilities.maf_index_by_uid(options.mafType, options.indexLocation) + else: + index = maf_utilities.maf_index_by_uid(options.mafType, options.mafIndexFile) + if index is None: + maf_utilities.tool_fail("The MAF source specified (%s) appears to be invalid." % (options.mafType)) + elif options.mafFile: + index, index_filename = maf_utilities.open_or_build_maf_index(options.mafFile, options.mafIndex, species=[dbkey]) + if index is None: + maf_utilities.tool_fail("Your MAF file appears to be malformed.") + else: + maf_utilities.tool_fail("Desired source MAF type has not been specified.") + + # Create MAF writter + out = bx.align.maf.Writer(open(output_file, "w")) + + # Iterate over input regions + num_blocks = 0 + num_regions = None + for num_regions, region in enumerate(bx.intervals.io.NiceReaderWrapper(open(interval_file, 'r'), chrom_col=chromCol, start_col=startCol, end_col=endCol, strand_col=strandCol, fix_strand=True, return_header=False, return_comments=False)): + src = maf_utilities.src_merge(dbkey, region.chrom) + for block in index.get_as_iterator(src, region.start, region.end): + if split_blocks_by_species: + blocks = [new_block for new_block in maf_utilities.iter_blocks_split_by_species(block) if maf_utilities.component_overlaps_region(new_block.get_component_by_src_start(dbkey), region)] + else: + blocks = [block] + for block in blocks: + block = maf_utilities.chop_block_by_region(block, src, region) + if block is not None: + if species is not None: + block = block.limit_to_species(species) + block = maf_utilities.orient_block_by_region(block, src, region) + if remove_all_gap_columns: + block.remove_all_gap_columns() + out.write(block) + num_blocks += 1 + + # Close output MAF + out.close() + + # remove index file if created during run + maf_utilities.remove_temp_index_file(index_filename) + + if num_blocks: + print("%i MAF blocks extracted for %i regions." % (num_blocks, (num_regions + 1))) + elif num_regions is not None: + print("No MAF blocks could be extracted for %i regions." % (num_regions + 1)) + else: + print("No valid regions have been provided.") + + +if __name__ == "__main__": + __main__() |
| b |
| diff -r 000000000000 -r cfea1d6354db interval2maf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/interval2maf.xml Fri Jul 17 10:56:42 2020 -0400 |
| [ |
| b'@@ -0,0 +1,289 @@\n+<tool id="Interval2Maf1" name="Extract MAF blocks" version="1.0.1">\n+ <description>given a set of genomic intervals</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <requirements>\n+ <expand macro="requirements" />\n+ </requirements>\n+ <command>\n+ <![CDATA[\n+ #if $maf_source_type.maf_source == "cached"\n+ #set $tab = \'\\t\'\n+ echo "$maf_source_type.mafType.fields.name${tab}$maf_source_type.mafType.fields.value${tab}$maf_source_type.mafType.fields.indexed_for${tab}$maf_source_type.mafType.fields.exists_in_maf${tab}$maf_source_type.mafType.fields.path" >> ./maf_indexes.loc &&\n+ #end if\n+ python \'$__tool_directory__/interval2maf.py\' \n+ --dbkey=${input1.dbkey} \n+ --chromCol=${input1.metadata.chromCol} \n+ --startCol=${input1.metadata.startCol} \n+ --endCol=${input1.metadata.endCol} \n+ --strandCol=${input1.metadata.strandCol}\n+ --interval_file=\'$input1\' \n+ --output_file=\'$out_file1\' \n+ --species=$maf_source_type.species \n+ --split_blocks_by_species=$split_blocks_by_species_selector.split_blocks_by_species\n+ #if $maf_source_type.maf_source == "user"\n+ --mafFile=\'$maf_source_type.mafFile\' \n+ --mafIndex=\'$maf_source_type.mafFile.metadata.maf_index\'\n+ #else\n+ --mafType=\'$maf_source_type.mafType\' \n+ --mafIndexFile=\'./maf_indexes.loc\' \n+ #end if\n+ #if $split_blocks_by_species_selector.split_blocks_by_species == "split_blocks_by_species"\n+ --remove_all_gap_columns=$split_blocks_by_species_selector.remove_all_gap_columns\n+ #end if\n+ ]]>\n+ </command>\n+ <inputs>\n+ <param format="interval" name="input1" type="data" label="Choose intervals">\n+ <validator type="unspecified_build" />\n+ </param>\n+ <conditional name="maf_source_type">\n+ <param name="maf_source" type="select" label="MAF Source">\n+ <option value="cached" selected="true">Locally Cached Alignments</option>\n+ <option value="user">Alignments in Your History</option>\n+ </param>\n+ <when value="user">\n+ <param format="maf" name="mafFile" label="Choose alignments" type="data">\n+ <options>\n+ <filter type="data_meta" ref="input1" key="dbkey" />\n+ </options>\n+ <validator type="dataset_ok_validator" />\n+ </param>\n+ <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment">\n+ <options>\n+ <filter type="data_meta" ref="mafFile" key="species" />\n+ </options>\n+ </param>\n+ </when>\n+ <expand macro="maf_source" />\n+ </conditional>\n+ <conditional name="split_blocks_by_species_selector">\n+ <param name="split_blocks_by_species" type="select" label="Split blocks by species" help="Not usually applicable. See help below for more information.">\n+ <option value="split_blocks_by_species">Split by species</option>\n+ <option value="dont_split_blocks_by_species" selected="true">Do not split</option>\n+ </param>\n+ <when value="dont_split_blocks_by_species">\n+ <!-- do nothing here -->\n+ </when>\n+ <when value="split_blocks_by_species">\n+ <param name="remove_all_gap_columns" type="select" label="Collapse empty alignment columns">\n+ <option value="remove_all_gap_columns" selected="true">Collapse empty columns</option>\n+ <option value="do_not_remove_all_gap_columns">Do not collapse</option>\n+ </param>\n+ </when>\n+ </conditional>\n+ </inputs>\n+ '..b'species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n+\n+ a score=2047408.0\n+ s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG\n+ s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG\n+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n+\n+ a score=2047408.0\n+ s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG\n+ s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG\n+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n+\n+ a score=2047408.0\n+ s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG\n+ s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG\n+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n+\n+ a score=2047408.0\n+ s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG\n+ s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG\n+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n+\n+ a score=2047408.0\n+ s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG\n+ s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG\n+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n+\n+ a score=2047408.0\n+ s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG\n+ s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG\n+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n+\n+ a score=2047408.0\n+ s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG\n+ s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG\n+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n+\n+ a score=2047408.0\n+ s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG\n+ s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG\n+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n+\n+ a score=2047408.0\n+ s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG\n+ s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG\n+ s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG\n+ ]]>\n+ </help>\n+ <expand macro="citations" />\n+</tool>\n' |
| b |
| diff -r 000000000000 -r cfea1d6354db macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Jul 17 10:56:42 2020 -0400 |
| b |
| @@ -0,0 +1,27 @@ +<macros> + <xml name="requirements"> + <requirement type="package" version="0.8.9">bx-python</requirement> + <yield /> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/btr398</citation> + </citations> + </xml> + <xml name="maf_source"> + <when value="cached"> + <param name="mafType" type="select" label="Choose alignments"> + <options from_data_table="maf_indexes"> + <filter type="data_meta" ref="input1" key="dbkey" column="2" multiple="True" separator=","/> + <validator type="no_options" message="No alignments are available for the build associated with the selected interval file"/> + </options> + </param> + <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment"> + <options from_data_table="maf_indexes"> + <column name="value" index="3"/> + <filter type="multiple_splitter" column="3" separator=","/> + </options> + </param> + </when> + </xml> +</macros> |
| b |
| diff -r 000000000000 -r cfea1d6354db test-data/interval2maf-in1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/interval2maf-in1.bed Fri Jul 17 10:56:42 2020 -0400 |
| b |
| @@ -0,0 +1,100 @@ +chr22 36937376 36938502 NM_000395.3_cds_13_0_chr22_36937377_f 0 + +chr22 37723184 37726503 NM_001039141.3_cds_6_0_chr22_37723185_f 0 + +chr22 37206546 37207803 NM_001051.5_cds_0_0_chr22_37206547_r 0 - +chr22 32190771 32191352 NM_001098527.3_cds_0_0_chr22_32190772_r 0 - +chr22 32358071 32358444 NM_001098535.1_cds_0_0_chr22_32358072_f 0 + +chr22 36265150 36266033 NM_001136540.1_cds_5_0_chr22_36265151_f 0 + +chr22 36265150 36266033 NM_001136541.1_cds_4_0_chr22_36265151_f 0 + +chr22 27982220 27983851 NM_001145418.1_cds_0_0_chr22_27982221_r 0 - +chr22 32190771 32191352 NM_001159545.2_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 NM_001159546.2_cds_0_0_chr22_32190772_r 0 - +chr22 18918315 18918491 NM_001195226.2_cds_3_0_chr22_18918316_r 0 - +chr22 37206546 37207803 NM_001278687.2_cds_0_0_chr22_37206547_r 0 - +chr22 17108306 17109820 NM_001289905.1_cds_11_0_chr22_17108307_f 0 + +chr22 42692889 42693951 NM_001318038.2_cds_0_0_chr22_42692890_r 0 - +chr22 26026444 26027678 NM_001318245.2_cds_42_0_chr22_26026445_f 0 + +chr22 21634684 21635644 NM_001331066.1_cds_3_0_chr22_21634685_f 0 + +chr22 42141151 42141396 NM_001348386.3_cds_2_0_chr22_42141152_r 0 - +chr22 36265150 36266033 NM_001362927.2_cds_4_0_chr22_36265151_f 0 + +chr22 32190771 32191352 NM_001364982.1_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 NM_001364983.1_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 NM_001364984.1_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 NM_001364985.1_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 NM_001364986.1_cds_0_0_chr22_32190772_r 0 - +chr22 23573265 23573585 NM_001369906.1_cds_0_0_chr22_23573266_r 0 - +chr22 27796762 27800543 NM_002430.3_cds_1_0_chr22_27796763_r 0 - +chr22 36265150 36266033 NM_003661.4_cds_5_0_chr22_36265151_f 0 + +chr22 21030830 21031812 NM_004173.3_cds_3_0_chr22_21030831_r 0 - +chr22 42209650 42215305 NM_005650.3_cds_4_0_chr22_42209651_r 0 - +chr22 46256560 46263322 NM_006071.2_cds_0_0_chr22_46256561_r 0 - +chr22 32358158 32358444 NM_006604.2_cds_1_0_chr22_32358159_f 0 + +chr22 38080839 38081679 NM_013356.2_cds_1_0_chr22_38080840_r 0 - +chr22 46363995 46364251 NM_014246.3_cds_1_0_chr22_46363996_r 0 - +chr22 46533626 46537170 NM_014246.3_cds_34_0_chr22_46533627_r 0 - +chr22 17108306 17109820 NM_014339.7_cds_12_0_chr22_17108307_f 0 + +chr22 36141199 36142058 NM_014349.3_cds_0_0_chr22_36141200_r 0 - +chr22 49883662 49887178 NM_014838.3_cds_1_0_chr22_49883663_f 0 + +chr22 17817310 17819129 NM_015241.3_cds_6_0_chr22_17817311_r 0 - +chr22 18918315 18918491 NM_016335.5_cds_3_0_chr22_18918316_r 0 - +chr22 42692889 42693951 NM_017436.7_cds_0_0_chr22_42692890_r 0 - +chr22 37655271 37655684 NM_018957.5_cds_17_0_chr22_37655272_f 0 + +chr22 23573265 23573585 NM_020070.4_cds_0_0_chr22_23573266_r 0 - +chr22 29441541 29442122 NM_021026.2_cds_1_0_chr22_29441542_f 0 + +chr22 29488848 29490703 NM_021076.4_cds_3_0_chr22_29488849_f 0 + +chr22 35726210 35727194 NM_030642.1_cds_2_0_chr22_35726211_f 0 + +chr22 36191074 36191912 NM_030643.4_cds_0_0_chr22_36191075_r 0 - +chr22 36141199 36142058 NM_030644.2_cds_0_0_chr22_36141200_r 0 - +chr22 17119390 17121127 NM_031890.4_cds_0_0_chr22_17119391_r 0 - +chr22 26026444 26027678 NM_032608.7_cds_42_0_chr22_26026445_f 0 + +chr22 22514001 22515630 NM_080740.5_cds_0_0_chr22_22514002_r 0 - +chr22 50546243 50549951 NM_138433.5_cds_0_0_chr22_50546244_f 0 + +chr22 36265150 36266033 NM_145343.2_cds_6_0_chr22_36265151_f 0 + +chr22 36141199 36142058 NM_145639.2_cds_0_0_chr22_36141200_r 0 - +chr22 36141199 36142058 NM_145640.2_cds_0_0_chr22_36141200_r 0 - +chr22 36191074 36191912 NM_145660.2_cds_0_0_chr22_36191075_r 0 - +chr22 21634684 21635266 NM_152612.3_cds_3_0_chr22_21634685_f 0 + +chr22 31712082 31717291 NM_173566.3_cds_5_0_chr22_31712083_r 0 - +chr22 42209650 42215305 NM_181492.2_cds_3_0_chr22_42209651_r 0 - +chr22 36937376 36938502 XM_005261340.3_cds_13_0_chr22_36937377_f 0 + +chr22 27982220 27983851 XM_005261405.2_cds_0_0_chr22_27982221_r 0 - +chr22 42692889 42693951 XM_005261644.2_cds_0_0_chr22_42692890_r 0 - +chr22 42692889 42693951 XM_005261646.4_cds_0_0_chr22_42692890_r 0 - +chr22 42209650 42215305 XM_005261722.3_cds_4_0_chr22_42209651_r 0 - +chr22 22646311 22646521 XM_005261815.3_cds_1_0_chr22_22646312_f 0 + +chr22 22646311 22646521 XM_005261818.2_cds_1_0_chr22_22646312_f 0 + +chr22 42209650 42215305 XM_006724313.3_cds_4_0_chr22_42209651_r 0 - +chr22 35726271 35727194 XM_006724321.4_cds_3_0_chr22_35726272_f 0 + +chr22 46363995 46364251 XM_006724383.3_cds_1_0_chr22_46363996_r 0 - +chr22 46533626 46537170 XM_006724383.3_cds_34_0_chr22_46533627_r 0 - +chr22 32190771 32191352 XM_011529826.2_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 XM_011529827.3_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 XM_011529828.2_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 XM_011529832.2_cds_0_0_chr22_32190772_r 0 - +chr22 42209650 42215305 XM_011530353.2_cds_4_0_chr22_42209651_r 0 - +chr22 42209650 42215305 XM_011530354.2_cds_3_0_chr22_42209651_r 0 - +chr22 26026444 26027678 XM_011530458.2_cds_43_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_011530459.2_cds_43_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_011530460.2_cds_42_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_011530461.2_cds_43_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_011530464.2_cds_43_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_011530465.2_cds_42_0_chr22_26026445_f 0 + +chr22 36265199 36266033 XM_011530478.2_cds_5_0_chr22_36265200_f 0 + +chr22 46533626 46537170 XM_011530553.1_cds_16_0_chr22_46533627_r 0 - +chr22 46363995 46364251 XM_011530554.2_cds_1_0_chr22_46363996_r 0 - +chr22 46363995 46364251 XM_011530555.2_cds_1_0_chr22_46363996_r 0 - +chr22 17119390 17121127 XM_011546124.2_cds_1_0_chr22_17119391_r 0 - +chr22 32358153 32358611 XM_017028534.1_cds_1_0_chr22_32358154_f 0 + +chr22 35726284 35727194 XM_017028945.2_cds_2_0_chr22_35726285_f 0 + +chr22 26026444 26027678 XM_017029012.1_cds_43_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_017029013.1_cds_43_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_017029014.1_cds_43_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_017029015.1_cds_42_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_017029016.1_cds_31_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_017029017.1_cds_41_0_chr22_26026445_f 0 + +chr22 18846931 18848320 XM_017029167.2_cds_0_0_chr22_18846932_f 0 + +chr22 23394179 23394792 XM_017029168.1_cds_3_0_chr22_23394180_f 0 + +chr22 23394222 23394792 XM_017029169.1_cds_2_0_chr22_23394223_f 0 + +chr22 50433133 50434498 XM_017029177.1_cds_0_0_chr22_50433134_r 0 - +chr22 50433133 50434498 XM_017029178.1_cds_0_0_chr22_50433134_r 0 - +chr22 36191074 36191842 XM_024452274.1_cds_0_0_chr22_36191075_r 0 - +chr22 49883662 49887178 XM_024452312.1_cds_1_0_chr22_49883663_f 0 + |
| b |
| diff -r 000000000000 -r cfea1d6354db test-data/interval2maf-in1.maf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/interval2maf-in1.maf Fri Jul 17 10:56:42 2020 -0400 |
| b |
| b'@@ -0,0 +1,6178 @@\n+##maf version=1\n+a score=19659433.0\n+s hg38.chr22 36937376 624 + 50818468 GGTGTTCCCTGTAGGATTCGGGGACAGCGAGGTGTCACCTCTCACCATAGAGGACCCCAAGCATGTCTGTGATCCACCATCTGGGCCTGACACGACTCCAGCTGCCTCAGATCTACCCACAGAGCAGCCCCCCAGCCCCCAGCCAGGCCCGCCTGCCGCCTCCCACACACCTGAGAAACAGGCTTCCAGCTTTGACTTCAATGGGCCCTACCTGGGGCCGCCCCACAGCCGCTCCCTACCTGACATCCTGGGCCAGCCGGAGCCCCCACAGGAGGGTGGGAGCCAGAAGTCCCCACCTCCAGGGTCCCTGGAGTACCTGTGTCTGCCTGCTGGGGGGCAGGTGCAACTGGTCCCTCTGGCCCAGGCGATGGGACCAGGACAGGCCGTGGAAGTGGAGAGAAGGCCGAGCCAGGGGGCTGCAGGGAGTCCCTCCCTGGAGTCCGGGGGAGGCCCTGCCCCTCCTGCTCTTGGGCCAAGGGTGGGAGGACAGGACCAAAAGGACAGCCCTGTGGCTATACCCATGAGCTCTGGGGACACTGAGGACCCTGGAGTGGCCTCTGGTTATGTCTCCTCTGCAGACCTGGTATTCACCCCAAACTCAGGGGCCTCGTCTGTCTCCCTAGT \n+s eulFla1.LGHW01004134v1 40149 624 + 294365 GGTCATCCCTGTAGGCTTCCAGGACATTGAGGTGTCACTTCTCATCACAGAGGACCCTAAAAGTGTCTGTGACCCACCATCGGGGCCTGATGTGACTCCGGCTGCCTCCGGCCAGCCCACAGAGCAGCCCTGCAGCCCTCCGCCGGCCCCGCCAGACCCCTCAGACAGACCTGAGAATCAGCTTTCCAGCTTCGACTTCAACGGCCCCTACCTGGGCCCACCCCGCAGCCACTCTCTGCCTGAACTCGTGGGCCAGCCGGTGCCCCCGCAGACGGGGGAGGGCCAGAAGCCGCCGCCCCCAGGGTCCCTGGAGTACCTGTGTTTGCCTGCTGGGGGGCAGGTGCAGCTGGTCCCACTGGCCCAGGTGGAGGGGCAGGGCCAGGTCATGGATGTGGAGCGAAGGCCCAGCCCGGGGCCCGAGGGGAGCCCCTCCTTGGAGCCCGGGGGAGGCCCCGACTCTCCTGCACTTGGGCCAAGGGTGGATGGACAGGGCCCAATGGACAGTCAAGTGGCTCTGTCCACGGGCTCTGGGGACCCTAAGGATGCTGCCGTGGCCTCTGGTTATATCCCCGCTGCAGACTTGTTGTTCACCCCAAGCTCAGGGGCCCTGTCTGTCTCCCCGGC \n+i eulFla1.LGHW01004134v1 C 0 C 0 \n+s mm10.chr15 78348071 612 + 104043685 GGAGTCATATGCACATTTGGAAGACAACAACGTGTCACCTCTCACTATAGAGGACCCTAATATAATTCGAGTTCCACCATCCGGGCCTGATACAACCCCAGCTGCCTCATCCGAATCCACAGAGCAACTTCCCAATGTTCAAGTAGAGGGACCAACTCCT---AACAGACCTAGGAAGCAATTACCCAGCTTTGACTTCAATGGGCCCTACCTGGGGCCTCCCCAATCCCACTCTCTGCCTGATCTCCCAGACCAGCTGGGTTCCCCCCAGGTGGGTGGGAGCCTGAAGCCAGCACTGCCAGGCTCCTTGGAGTACATGTGTCTGCCCCCTGGAGGTCAAGCGCAACTGGTTCCATTGTCCCAGGTGATGGGGCAGGGCCAGGCTATGGATGTGCAGTGTGGGTCCAGCCTGGAGACCTCAGGGAGCCCTTCTGTGGAGCCAAAGGAGAAC---------CCTCCAGTTGAGCTGAGCATGGAGGAACAGGAGGCACGGGACAACCCAGTGACTCTGCCCATAAGCTCTGGGGGCCCTGAGGGCAGTATGATGGCCTCTGATTATGTCACTCCTGGAGATCCGGTGCTCACTCTGCCCACAGGGCCCCTGTCTACCTCTCTGGG \n+i mm10.chr15 C 0 C 0 \n+\n+a score=1807111.0\n+s hg38.chr22 36938000 64 + 50818468 TCCCTCTCTGGGCCTCCCCTCAGACCAGACCCCCAGCTTATGTCCTGGGCTGGCCAGTGGACCC \n+s eulFla1.LGHW01004134v1 40773 64 + 294365 TCCCCCTCTGGGCCACTGCTCAGACCCGAGCCCCAGCCTGTGTCCTGGGCCAGCCGAGGGGCCT \n+i eulFla1.LGHW01004134v1 C 0 C 0 \n+s mm10.chr15 78348683 64 + 104043685 CCCCTCTCTAGGGTTGCCCTCAGCCCAAAGCCCCAGTCTCTGTCTTAAGCTGCCCAGGGTCCCC \n+i mm10.chr15 C 0 C 0 '..b'AGTGTAACTTCAGAGAATTGATCAGCTGTGACCAGTGGGAGGTCATGCAGTCTGTGTGCCATGTGCTGAGACCATTTGATGCTGCAAGCCGAGAGATGAGTGCCCACATGTCTACGCTGAGCCAGGTCATCCCCATGATCCACATCCTCAGCAGAAAAGTGGAGATGCTGTTTGGGGAGACCATGGGCATTGACACCATGCTTAAGTCCCTGAAGGAAGCCATGGCAAGCCGCCTGTCTGCCACACTCCATGACCCCAGGTACATCTTTGCCACACTGCTGGACCCTCGCTACAAAGCTTCCCTGTTCACAGAGGAGGAGGCAGAGCAGTACAGGCAAGACTTAATCAGGGAGCTAGAAATACTGAATTCTACCTCAGAGGACACTGCCACCTCCAATGGCTGTGACTCAGGGTCCCCACTTAAAGACACTGGCACAGAGGAGAGCCTGTGGTCACTCGCACC------GATAAAGAGAGATCAGAGAGAGAAGCTACCTGAAGACATGGTGCTTGCGTATTTGGAGGAAGAGGTGCTGGAACACAGCTGTGACCCACTCACCTACTGGAACCTAAAGCGGTCATCGTGGCCTGGGCTGTCTACCTTAGCAGTTCGATTTCTGGGATGTCCCCCAAGTACAGTCCCCTCAGAAAAGCTGTTCAGCACACCCATGGATGCTGGCAGCTTTGGCCAGCCCAGGCTCATGATGGAGCATTTTGAAAAGCTCATCTTTTTAAAAGTGAATCTTCCTTTAATATGCTTTCAGTATTGA \n+i mm10.chr15 C 0 C 0 \n+\n' |
| b |
| diff -r 000000000000 -r cfea1d6354db test-data/interval2maf-in1.maf.index |
| b |
| Binary file test-data/interval2maf-in1.maf.index has changed |
| b |
| diff -r 000000000000 -r cfea1d6354db test-data/interval2maf-in2.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/interval2maf-in2.bed Fri Jul 17 10:56:42 2020 -0400 |
| b |
| @@ -0,0 +1,51 @@ +chr22 17119390 17121127 XM_011546124.2_cds_1_0_chr22_17119391_r 0 - +chr22 17817310 17819129 NM_015241.3_cds_6_0_chr22_17817311_r 0 - +chr22 18846931 18848320 XM_017029167.2_cds_0_0_chr22_18846932_f 0 + +chr22 18918315 18918491 NM_016335.5_cds_3_0_chr22_18918316_r 0 - +chr22 18918315 18918491 NM_001195226.2_cds_3_0_chr22_18918316_r 0 - +chr22 21030830 21031812 NM_004173.3_cds_3_0_chr22_21030831_r 0 - +chr22 21634684 21635644 NM_001331066.1_cds_3_0_chr22_21634685_f 0 + +chr22 21634684 21635266 NM_152612.3_cds_3_0_chr22_21634685_f 0 + +chr22 22514001 22515630 NM_080740.5_cds_0_0_chr22_22514002_r 0 - +chr22 22646311 22646521 XM_005261818.2_cds_1_0_chr22_22646312_f 0 + +chr22 22646311 22646521 XM_005261815.3_cds_1_0_chr22_22646312_f 0 + +chr22 23394179 23394792 XM_017029168.1_cds_3_0_chr22_23394180_f 0 + +chr22 23394222 23394792 XM_017029169.1_cds_2_0_chr22_23394223_f 0 + +chr22 23573265 23573585 NM_001369906.1_cds_0_0_chr22_23573266_r 0 - +chr22 23573265 23573585 NM_020070.4_cds_0_0_chr22_23573266_r 0 - +chr22 26026444 26027678 XM_011530458.2_cds_43_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_017029014.1_cds_43_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_017029015.1_cds_42_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_017029016.1_cds_31_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_017029013.1_cds_43_0_chr22_26026445_f 0 + +chr22 26026444 26027678 NM_032608.7_cds_42_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_017029012.1_cds_43_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_011530465.2_cds_42_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_011530464.2_cds_43_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_011530461.2_cds_43_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_011530460.2_cds_42_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_011530459.2_cds_43_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_017029017.1_cds_41_0_chr22_26026445_f 0 + +chr22 26026444 26027678 NM_001318245.2_cds_42_0_chr22_26026445_f 0 + +chr22 27796762 27800543 NM_002430.3_cds_1_0_chr22_27796763_r 0 - +chr22 27982220 27983851 XM_005261405.2_cds_0_0_chr22_27982221_r 0 - +chr22 27982220 27983851 NM_001145418.1_cds_0_0_chr22_27982221_r 0 - +chr22 29441541 29442122 NM_021026.2_cds_1_0_chr22_29441542_f 0 + +chr22 29488848 29490703 NM_021076.4_cds_3_0_chr22_29488849_f 0 + +chr22 31712082 31717291 NM_173566.3_cds_5_0_chr22_31712083_r 0 - +chr22 32190771 32191352 NM_001364983.1_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 XM_011529832.2_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 NM_001159545.2_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 XM_011529828.2_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 NM_001159546.2_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 NM_001364986.1_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 NM_001098527.3_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 XM_011529826.2_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 NM_001364985.1_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 NM_001364982.1_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 XM_011529827.3_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 NM_001364984.1_cds_0_0_chr22_32190772_r 0 - +chr22 32358071 32358444 NM_001098535.1_cds_0_0_chr22_32358072_f 0 + +chr22 32358153 32358611 XM_017028534.1_cds_1_0_chr22_32358154_f 0 + +chr22 32358158 32358444 NM_006604.2_cds_1_0_chr22_32358159_f 0 + +chr22 35726210 35727194 NM_030642.1_cds_2_0_chr22_35726211_f 0 + |
| b |
| diff -r 000000000000 -r cfea1d6354db test-data/interval2maf-in3.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/interval2maf-in3.bed Fri Jul 17 10:56:42 2020 -0400 |
| b |
| @@ -0,0 +1,31 @@ +chr22 32190771 32191352 XM_011529826.2_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 NM_001364985.1_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 NM_001364982.1_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 XM_011529827.3_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 NM_001364984.1_cds_0_0_chr22_32190772_r 0 - +chr22 32358071 32358444 NM_001098535.1_cds_0_0_chr22_32358072_f 0 + +chr22 32358153 32358611 XM_017028534.1_cds_1_0_chr22_32358154_f 0 + +chr22 32358158 32358444 NM_006604.2_cds_1_0_chr22_32358159_f 0 + +chr22 35726210 35727194 NM_030642.1_cds_2_0_chr22_35726211_f 0 + +chr22 35726271 35727194 XM_006724321.4_cds_3_0_chr22_35726272_f 0 + +chr22 35726284 35727194 XM_017028945.2_cds_2_0_chr22_35726285_f 0 + +chr22 36141199 36142058 NM_145640.2_cds_0_0_chr22_36141200_r 0 - +chr22 36141199 36142058 NM_145639.2_cds_0_0_chr22_36141200_r 0 - +chr22 36141199 36142058 NM_014349.3_cds_0_0_chr22_36141200_r 0 - +chr22 36141199 36142058 NM_030644.2_cds_0_0_chr22_36141200_r 0 - +chr22 36191074 36191912 NM_145660.2_cds_0_0_chr22_36191075_r 0 - +chr22 36191074 36191912 NM_030643.4_cds_0_0_chr22_36191075_r 0 - +chr22 36191074 36191842 XM_024452274.1_cds_0_0_chr22_36191075_r 0 - +chr22 36265150 36266033 NM_001362927.2_cds_4_0_chr22_36265151_f 0 + +chr22 36265150 36266033 NM_003661.4_cds_5_0_chr22_36265151_f 0 + +chr22 36265150 36266033 NM_001136540.1_cds_5_0_chr22_36265151_f 0 + +chr22 36265150 36266033 NM_001136541.1_cds_4_0_chr22_36265151_f 0 + +chr22 36265150 36266033 NM_145343.2_cds_6_0_chr22_36265151_f 0 + +chr22 36265199 36266033 XM_011530478.2_cds_5_0_chr22_36265200_f 0 + +chr22 36937376 36938502 XM_005261340.3_cds_13_0_chr22_36937377_f 0 + +chr22 36937376 36938502 NM_000395.3_cds_13_0_chr22_36937377_f 0 + +chr22 37206546 37207803 NM_001278687.2_cds_0_0_chr22_37206547_r 0 - +chr22 37206546 37207803 NM_001051.5_cds_0_0_chr22_37206547_r 0 - +chr22 37655271 37655684 NM_018957.5_cds_17_0_chr22_37655272_f 0 + +chr22 37723184 37726503 NM_001039141.3_cds_6_0_chr22_37723185_f 0 + +chr22 38080839 38081679 NM_013356.2_cds_1_0_chr22_38080840_r 0 - |
| b |
| diff -r 000000000000 -r cfea1d6354db test-data/interval2maf-out1.maf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/interval2maf-out1.maf Fri Jul 17 10:56:42 2020 -0400 |
| b |
| b'@@ -0,0 +1,17038 @@\n+##maf version=1\n+a score=19659433.0\n+s hg38.chr22 36937376 624 + 50818468 GGTGTTCCCTGTAGGATTCGGGGACAGCGAGGTGTCACCTCTCACCATAGAGGACCCCAAGCATGTCTGTGATCCACCATCTGGGCCTGACACGACTCCAGCTGCCTCAGATCTACCCACAGAGCAGCCCCCCAGCCCCCAGCCAGGCCCGCCTGCCGCCTCCCACACACCTGAGAAACAGGCTTCCAGCTTTGACTTCAATGGGCCCTACCTGGGGCCGCCCCACAGCCGCTCCCTACCTGACATCCTGGGCCAGCCGGAGCCCCCACAGGAGGGTGGGAGCCAGAAGTCCCCACCTCCAGGGTCCCTGGAGTACCTGTGTCTGCCTGCTGGGGGGCAGGTGCAACTGGTCCCTCTGGCCCAGGCGATGGGACCAGGACAGGCCGTGGAAGTGGAGAGAAGGCCGAGCCAGGGGGCTGCAGGGAGTCCCTCCCTGGAGTCCGGGGGAGGCCCTGCCCCTCCTGCTCTTGGGCCAAGGGTGGGAGGACAGGACCAAAAGGACAGCCCTGTGGCTATACCCATGAGCTCTGGGGACACTGAGGACCCTGGAGTGGCCTCTGGTTATGTCTCCTCTGCAGACCTGGTATTCACCCCAAACTCAGGGGCCTCGTCTGTCTCCCTAGT \n+s eulFla1.LGHW01004134v1 40149 624 + 294365 GGTCATCCCTGTAGGCTTCCAGGACATTGAGGTGTCACTTCTCATCACAGAGGACCCTAAAAGTGTCTGTGACCCACCATCGGGGCCTGATGTGACTCCGGCTGCCTCCGGCCAGCCCACAGAGCAGCCCTGCAGCCCTCCGCCGGCCCCGCCAGACCCCTCAGACAGACCTGAGAATCAGCTTTCCAGCTTCGACTTCAACGGCCCCTACCTGGGCCCACCCCGCAGCCACTCTCTGCCTGAACTCGTGGGCCAGCCGGTGCCCCCGCAGACGGGGGAGGGCCAGAAGCCGCCGCCCCCAGGGTCCCTGGAGTACCTGTGTTTGCCTGCTGGGGGGCAGGTGCAGCTGGTCCCACTGGCCCAGGTGGAGGGGCAGGGCCAGGTCATGGATGTGGAGCGAAGGCCCAGCCCGGGGCCCGAGGGGAGCCCCTCCTTGGAGCCCGGGGGAGGCCCCGACTCTCCTGCACTTGGGCCAAGGGTGGATGGACAGGGCCCAATGGACAGTCAAGTGGCTCTGTCCACGGGCTCTGGGGACCCTAAGGATGCTGCCGTGGCCTCTGGTTATATCCCCGCTGCAGACTTGTTGTTCACCCCAAGCTCAGGGGCCCTGTCTGTCTCCCCGGC \n+i eulFla1.LGHW01004134v1 C 0 C 0 \n+s mm10.chr15 78348071 612 + 104043685 GGAGTCATATGCACATTTGGAAGACAACAACGTGTCACCTCTCACTATAGAGGACCCTAATATAATTCGAGTTCCACCATCCGGGCCTGATACAACCCCAGCTGCCTCATCCGAATCCACAGAGCAACTTCCCAATGTTCAAGTAGAGGGACCAACTCCT---AACAGACCTAGGAAGCAATTACCCAGCTTTGACTTCAATGGGCCCTACCTGGGGCCTCCCCAATCCCACTCTCTGCCTGATCTCCCAGACCAGCTGGGTTCCCCCCAGGTGGGTGGGAGCCTGAAGCCAGCACTGCCAGGCTCCTTGGAGTACATGTGTCTGCCCCCTGGAGGTCAAGCGCAACTGGTTCCATTGTCCCAGGTGATGGGGCAGGGCCAGGCTATGGATGTGCAGTGTGGGTCCAGCCTGGAGACCTCAGGGAGCCCTTCTGTGGAGCCAAAGGAGAAC---------CCTCCAGTTGAGCTGAGCATGGAGGAACAGGAGGCACGGGACAACCCAGTGACTCTGCCCATAAGCTCTGGGGGCCCTGAGGGCAGTATGATGGCCTCTGATTATGTCACTCCTGGAGATCCGGTGCTCACTCTGCCCACAGGGCCCCTGTCTACCTCTCTGGG \n+i mm10.chr15 C 0 C 0 \n+\n+a score=19659433.0\n+s hg38.chr22 36937376 624 + 50818468 GGTGTTCCCTGTAGGATTCGGGGACAGCGAGGTGTCACCTCTCACCATAGAGGACCCCAAGCATGTCTGTGATCCACCATCTGGGCCTGACACGACTCCAGCTGCCTCAGATCTACCCACAGAGCAGCCCCCCAGCCCCCAGCCAGGCCCGCCTGCCGCCTCCCACACACCTGAGAAACAGGCTTCCAGCTTTGACTTCAATGGGCCCTACCTGGGGCCGCCCCACAGCCGCTCCCTACCTGACATCCTGGGCCAGCCGGAGCCCCCACAGGAGGGTGGGAGCCAGAAGTCCCCACCTCCAGGGTCCCTGGAGTACCTGTGTCTGCCTGCTGGGGGGCAGGTGCAACTGGTCCCTCTGGCCCAGGCGATGGGACCAGGACAGGCCGTGGAAGTGGAGAGAAGGCCGAGCCAGGGGGCTGCAGGGAGTCCCTCCCTGGAGTCCGGGGGAGGCCCTGCCCCTCCTGCTCTTGGGCCAAGGGTGGGA'..b'AGTGTAACTTCAGAGAATTGATCAGCTGTGACCAGTGGGAGGTCATGCAGTCTGTGTGCCATGTGCTGAGACCATTTGATGCTGCAAGCCGAGAGATGAGTGCCCACATGTCTACGCTGAGCCAGGTCATCCCCATGATCCACATCCTCAGCAGAAAAGTGGAGATGCTGTTTGGGGAGACCATGGGCATTGACACCATGCTTAAGTCCCTGAAGGAAGCCATGGCAAGCCGCCTGTCTGCCACACTCCATGACCCCAGGTACATCTTTGCCACACTGCTGGACCCTCGCTACAAAGCTTCCCTGTTCACAGAGGAGGAGGCAGAGCAGTACAGGCAAGACTTAATCAGGGAGCTAGAAATACTGAATTCTACCTCAGAGGACACTGCCACCTCCAATGGCTGTGACTCAGGGTCCCCACTTAAAGACACTGGCACAGAGGAGAGCCTGTGGTCACTCGCACC------GATAAAGAGAGATCAGAGAGAGAAGCTACCTGAAGACATGGTGCTTGCGTATTTGGAGGAAGAGGTGCTGGAACACAGCTGTGACCCACTCACCTACTGGAACCTAAAGCGGTCATCGTGGCCTGGGCTGTCTACCTTAGCAGTTCGATTTCTGGGATGTCCCCCAAGTACAGTCCCCTCAGAAAAGCTGTTCAGCACACCCATGGATGCTGGCAGCTTTGGCCAGCCCAGGCTCATGATGGAGCATTTTGAAAAGCTCATCTTTTTAAAAGTGAATCTTCCTTTAATATGCTTTCAGTATTGA \n+i mm10.chr15 C 0 C 0 \n+\n' |
| b |
| diff -r 000000000000 -r cfea1d6354db test-data/interval2maf-out2.maf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/interval2maf-out2.maf Fri Jul 17 10:56:42 2020 -0400 |
| b |
| b'@@ -0,0 +1,7227 @@\n+##maf version=1\n+a score=5126687.0\n+s hg38.chr22 33698927 151 - 50818468 GGCCAGAGGGGGCTACGGTGCTCCGCCCTCCGCCCCTCCACCACCTCCGCCACCACC---TCAGGGAGGCTCCCAGCTGGGCCACTGCATCTCGGAGAACGAGGGGGGTGCTCATGGCTATGTCAACACCCTGGCTGTGGCCTCTCAGAATTGA \n+s eulFla1.LGHW01008773v1 48579 151 - 91162 GGCCAGAGCGGGTTACGGcgccccgccctccgccccgccgccacctccgcctccacc---tcAGGGAGGCTCCCAGCTGGGCCACTGCATCTCGGAGAACGAGGGGGGCGCCCACGGCTATGTCAACACTCTGGCGGTGGCCTCCCAGAATTGA \n+s mm10.chr6 29244363 148 - 149736546 GGCCAGAAGCAGCTATGGTGCTCCTCCCTCTGCCCCTCCCCCACCTCCACCACCACCACCTCAGGGAGGCTCCCAGCGGGGCCACT------TGGAAAATGAAGGGGGCCCTCATGGCTATGTCAACACTCTAGCTGTTGCCTCTCAGAATTGA \n+\n+a score=3181394.0\n+s hg38.chr22 33698828 99 - 50818468 CTCCATCTTCATGCTCAAGAACCTCTTCTTCCTCGGCTGCCGGGGCCTGGAGGCCCTGGAGGGCTGCTGGGACCGGGGCAATCGGGCCTCCCCGAGTCG \n+s eulFla1.LGHW01008773v1 48480 99 - 91162 CTCCGTCTTCATGCTCAAGAACCTCTTCTTCCTTGGCTGCCGCGGCCTGGAGGCCCTGGAGGGCTGCTGGGACCGGGGCGGCCGGGCCTCCCCTAGTCG \n+s mm10.chr6 29244264 99 - 149736546 GTCCATCTTTATGCTCAAGAATCTCTTTTTCCTTGGCTGCCGTGGCCTGGAGGCCTTGGAGGGCTGCTGGGACCGGGGGAGTTGGGTATCCCCAAGTCG \n+\n+a score=8321735.0\n+s hg38.chr22 33698587 241 - 50818468 GCCGCGTGCCGCTGCCCGCGCACCTGCGCTACCTGCTTATCGCCGTCTACTTCCTCACCCTCGCCTCGCCGGTGCTCTGGCTCTACGAGCTCAACGCCGCGGCCGCAGCGGCTGCATCCTGGGGCCAGGCCTCCGGGCCTGGCAGCTGCAGCCGCCTTCTGCGCCTGCTGGGCGGCTGCCTGGTGGACGTGCCCTTGCTGGCGCTGCGCTGCCTCCTGGTGGTCAGCTACCAGCAGCCCCT \n+s eulFla1.LGHW01008773v1 48254 226 - 91162 GCCGCGTGCCGCTGCCCGCGCACCTGCGCTACCTGCTCATCGCCGTCTACTTCCTCACGCTCGCCTCGCCGGTGCTCTGGCTCTACGAACTCAACGCC---------------TCGTCCTGGGGCCAGGCCTCGGGGCCCGGCAGCTGCAGCCGCCTCCTGCGCCTGCTGGGCGGCTGCCTGGTGGACGTGCCCTTGCTGGCCCTGCGCTGCCTCCTAGTGGTGAGCTACCAGCAGCCCCT \n+s mm10.chr6 29244026 238 - 149736546 GCCGCGTGCCGCTTCCGGCGCACCTGCGCTACCTGCTCATCGCCGTCTACTTCCTCACTCTTGCCTCCCCAGTGCTCTGGCTGTACGAGCTGAACACT---GCCACAGCAGCTCCGTCCTGGGGTCAGACCTCCGGGCCCGGAAGCTGCAGCCGCCTTTTACGTTTGCTGGGCGGCTGCCTGGTGGACGTGCCCTTGCTGGCGCTGCGCAGCCTCCTGGTCGTGAGCTACCAACAGCCGCT \n+\n+a score=3395583.0\n+s hg38.chr22 33698483 104 - 50818468 ACCCCTGCTGCTGCAGCCCCAGCGGCACCGCGCGGCCGGATGCTTCCTGGGCACGTGCTTGGACCTGCTCGACAGCTTCACGCTGGTGGAGCTGATGCTGGAGG \n+s eulFla1.LGHW01008773v1 48150 104 - 91162 ACCCCTGCTGCTGCAGCCCCAGCGGCACCGCGCCGCCGGCTGCTTCCTGGGCACGTGTCTGGACCTGCTCGACAGCTTCACCCTGGTGGAGCTGACGCTGGAAG \n+s mm10.chr6 29243922 104 - 149736546 TCCCCTGCTCCTGCAGCCACAGCAGCATCGCGCCGCGGGCTGCTTCCTGGGCACGTGTCTGGACCTGCTGGACAGCTTTACACTGGTGGAGCTGATGCTGGACG \n+\n+a score=2062525.0\n+s hg38.chr22 33698413 70 - 50818468 TGTCGGTGCCCCTGCTCTACAGCTTGGTGCGGGCCATCAGCGAGGCGGGCGCGCCCCCGGGATCGGCAGG \n+s eulFla1.LGHW01008773v1 48080 70 - 91162 TGTCGGTGCCCCTGCTCTACAGCTTGGTGCGGGCCATCAGCGAGGCGGGCGCCCCGCCGGGCTCTGCGGG \n+s mm10.chr6 29243852 70 - 149736546 TGTCCGTGCCGCTGCTCTACAGCCTAGTGCGTGCCATTAGCGAGGCGGGCGCGCCCCCGGGCTCGGCGGG \n+\n+a score=4187755.0\n+s hg38.chr22 33698268 145 - 50818468 GAGTTCGCCTTCGCCTACCTGGCCTGGCTTATCTACTCCATCGCCTTCACTCCCAAGGTGGTGCTGATCCTGGGCACGTCCATCCTAGACCTCATCGAGCTACGCGCGCCCTTCGGCACCACGGGCTTCCGTCTCACCATGGCGC \n+s eulFla1.LGHW01008773v1 47935 145 - 91162 GAGTTCGCCTTCGCCTACCTGGCCTGGCTCATCTACTCCATCGCCTTCACGCCCAAGGTGGTGCTTATCCTGGGCACGTCCATCCTGGACCTCATCGAGCTGCGCGCGCCCTTCGGCACCACCGGCTTCCGCCTCACCATGGCGC \n+s mm10.chr6 29243707 145 - 149736546 GAGTTCGCTTTTGCGTACCTGGCCTGGCTCATCTACTCCATCGCTTTCACCCCTAAGGTGGTGCTCATCCTGGGCACATCCATCCTGGACCTCATCGAGCTGCGCGCGCCCTTTGGCACCACGGGCTTTCGCCTTACCATGGCGC \n+\n+a score=491529.0\n+s hg38.chr22 33698246 22 - 50818468 GGGGGCGGCCGCGGCAGCGGGC \n+s eulFla1.LGHW01008773v1 47913 22 - 91162 GGCGGCGGCCGGGGCAACCGGC \n+s mm10.chr6 29243685 22 - 149736546 GGGGACGACTGGGGCAGCGGGC \n+\n+a score=17457.0\n+s hg38.chr22 33698245 1 - 50818468 T \n+s eulFla1.LGHW01008773v1 47912 1 - 91162 T \n+s mm10.chr6 29243684 1 - 149736546 C \n+\n+a score=263332.0\n+s hg38.chr22 '..b'TACCAGATGGCCAAATCCAACTCTGGCTTCATGGCTATGGTCAAGAATTTTGTGGCCAAGAGACACATCCCTTTCTGGACGGCTAGAGGGGTGCAGAGAGCCTTTGAGGGCACAACTCTGGCCATGACCAATGGTGCCTGGGTGATGGGTGCTGCTGGGGCTGGCTTCTTACTTATGAAAGAC \n+s eulFla1.LGHW01001967v1 331725 189 + 548553 CGTGCCCACCAGATGGCCAAAGCTAACCTTGGCTTCATGGCTATGGTCAAGAATTTTGTGGCCACACACAACATCTCTTTCTGGAAGCCAGGAGAGGTGCAGACAATCTTTGTAGATGCAACTCTGGCGGTGACCAAGGGTGCCCAGGGGATGGGTGCTGCTGGGGCTGGCCTCTTTCTTATGCAAGAT \n+i eulFla1.LGHW01001967v1 C 0 C 0 \n+\n+a score=10960.0\n+s hg38.chr22 35726986 1 + 50818468 A \n+s eulFla1.LGHW01001967v1 331914 1 + 548553 G \n+i eulFla1.LGHW01001967v1 C 0 C 0 \n+\n+a score=10960.0\n+s hg38.chr22 35726986 1 + 50818468 A \n+s eulFla1.LGHW01001967v1 331914 1 + 548553 G \n+i eulFla1.LGHW01001967v1 C 0 C 0 \n+\n+a score=10960.0\n+s hg38.chr22 35726986 1 + 50818468 A \n+s eulFla1.LGHW01001967v1 331914 1 + 548553 G \n+i eulFla1.LGHW01001967v1 C 0 C 0 \n+\n+a score=2757722.0\n+s hg38.chr22 35726987 103 + 50818468 TGAGCAGCTTCCTGCAGAGCTGGAAGCACCTGGAGGATGGGGCAAGGACGGAGACAGCAGAGGAACTGAGAGCACTTGCTAAGAAGCTGGAGCAGGAGCTGGA \n+s eulFla1.LGHW01001967v1 331915 103 + 548553 TGGGCAAACTTCTGCAGAACTGGAAGCACCTGGAGGAGGGGGCGAGGGCAGAGACAGCCAAGGAACTGAGGACACTTGCCAAGGAGCAGGAGCAGGAGCTGAG \n+i eulFla1.LGHW01001967v1 C 0 C 0 \n+\n+a score=2757722.0\n+s hg38.chr22 35726987 103 + 50818468 TGAGCAGCTTCCTGCAGAGCTGGAAGCACCTGGAGGATGGGGCAAGGACGGAGACAGCAGAGGAACTGAGAGCACTTGCTAAGAAGCTGGAGCAGGAGCTGGA \n+s eulFla1.LGHW01001967v1 331915 103 + 548553 TGGGCAAACTTCTGCAGAACTGGAAGCACCTGGAGGAGGGGGCGAGGGCAGAGACAGCCAAGGAACTGAGGACACTTGCCAAGGAGCAGGAGCAGGAGCTGAG \n+i eulFla1.LGHW01001967v1 C 0 C 0 \n+\n+a score=2757722.0\n+s hg38.chr22 35726987 103 + 50818468 TGAGCAGCTTCCTGCAGAGCTGGAAGCACCTGGAGGATGGGGCAAGGACGGAGACAGCAGAGGAACTGAGAGCACTTGCTAAGAAGCTGGAGCAGGAGCTGGA \n+s eulFla1.LGHW01001967v1 331915 103 + 548553 TGGGCAAACTTCTGCAGAACTGGAAGCACCTGGAGGAGGGGGCGAGGGCAGAGACAGCCAAGGAACTGAGGACACTTGCCAAGGAGCAGGAGCAGGAGCTGAG \n+i eulFla1.LGHW01001967v1 C 0 C 0 \n+\n+a score=841012.0\n+s hg38.chr22 35727090 49 + 50818468 CCGGCTCACCCAGCACCACCGGCACCTGCCGCAGAAGGCGAGCCAGACC \n+s eulFla1.LGHW01001967v1 332018 49 + 548553 GCAGCTCGCCGAGCGCTACCAGGACCTGCAGCAGAAGGCGAGCCAGACC \n+i eulFla1.LGHW01001967v1 C 0 I 915 \n+\n+a score=841012.0\n+s hg38.chr22 35727090 49 + 50818468 CCGGCTCACCCAGCACCACCGGCACCTGCCGCAGAAGGCGAGCCAGACC \n+s eulFla1.LGHW01001967v1 332018 49 + 548553 GCAGCTCGCCGAGCGCTACCAGGACCTGCAGCAGAAGGCGAGCCAGACC \n+i eulFla1.LGHW01001967v1 C 0 I 915 \n+\n+a score=841012.0\n+s hg38.chr22 35727090 49 + 50818468 CCGGCTCACCCAGCACCACCGGCACCTGCCGCAGAAGGCGAGCCAGACC \n+s eulFla1.LGHW01001967v1 332018 49 + 548553 GCAGCTCGCCGAGCGCTACCAGGACCTGCAGCAGAAGGCGAGCCAGACC \n+i eulFla1.LGHW01001967v1 C 0 I 915 \n+\n+a score=668337.0\n+s hg38.chr22 35727139 55 + 50818468 TGTTCCAGCTCCCGGGGCAGGGCTGTTCGAGGATCCCGTGTGGTTAAACCAGAAG \n+\n+a score=668337.0\n+s hg38.chr22 35727139 55 + 50818468 TGTTCCAGCTCCCGGGGCAGGGCTGTTCGAGGATCCCGTGTGGTTAAACCAGAAG \n+\n+a score=668337.0\n+s hg38.chr22 35727139 55 + 50818468 TGTTCCAGCTCCCGGGGCAGGGCTGTTCGAGGATCCCGTGTGGTTAAACCAGAAG \n+\n' |
| b |
| diff -r 000000000000 -r cfea1d6354db test-data/interval2maf-out3.maf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/interval2maf-out3.maf Fri Jul 17 10:56:42 2020 -0400 |
| b |
| b'@@ -0,0 +1,7128 @@\n+##maf version=1\n+a score=196573.0\n+s hg38.chr22 18627690 7 - 50818468 CAAATAA \n+\n+a score=196573.0\n+s hg38.chr22 18627690 7 - 50818468 CAAATAA \n+\n+a score=196573.0\n+s hg38.chr22 18627690 7 - 50818468 CAAATAA \n+\n+a score=196573.0\n+s hg38.chr22 18627690 7 - 50818468 CAAATAA \n+\n+a score=196573.0\n+s hg38.chr22 18627690 7 - 50818468 CAAATAA \n+\n+a score=196573.0\n+s hg38.chr22 18627690 7 - 50818468 CAAATAA \n+\n+a score=196573.0\n+s hg38.chr22 18627690 7 - 50818468 CAAATAA \n+\n+a score=196573.0\n+s hg38.chr22 18627690 7 - 50818468 CAAATAA \n+\n+a score=196573.0\n+s hg38.chr22 18627690 7 - 50818468 CAAATAA \n+\n+a score=196573.0\n+s hg38.chr22 18627690 7 - 50818468 CAAATAA \n+\n+a score=196573.0\n+s hg38.chr22 18627690 7 - 50818468 CAAATAA \n+\n+a score=196573.0\n+s hg38.chr22 18627690 7 - 50818468 CAAATAA \n+\n+a score=6623803.0\n+s hg38.chr22 18627116 574 - 50818468 TGGATATGACCTTGGATGCCAACACAGCCAACAACTTCCTCCTCATTTCTGACGACCTCAGGAGCGTCCGAAGTGGGCGCATCAGACAGAATCGGCAAGACCTTGCCGAGAGATTTGACGTGTCCGTTTGCATCCTGGGCTCCCCTCGCTTTACCTGTGGCCGCCACTGCTGGGAGGTGGACGTGGGAACAAGCACAGAATGGGACCTGGGAGTCTGCAGAGAATCTGTTCACCGCAAAGGGAGGATCCAGCTGACCACAGAGCTTGGATTCTGGACTGTGAGTTTGAGGGATGGAGGCCGCCTCTCTGCCACCACGGTGCCGCTGACTTTCCTCTTCGTAGACCGCAAGTTACAGCGAGTGGGGATTTTTCTGGATATGGGCATGCAGAACGTTTCCTTTTTTGATGCTGAAAGTGGTTCCCATGTCTATACATTCAGGAGCGTATCTGCTGAGGAGCCATTGCGCCCATTTTTGGCTCCTTCAGTTCCACCTAATGGTGATCAAGGTGTCTTGAGCATCTGTCCTTTGATGAACTCAGGCACTACTGATGCTCCAGTCCGTCCTGGGGAGGC \n+\n+a score=6623803.0\n+s hg38.chr22 18627116 574 - 50818468 TGGATATGACCTTGGATGCCAACACAGCCAACAACTTCCTCCTCATTTCTGACGACCTCAGGAGCGTCCGAAGTGGGCGCATCAGACAGAATCGGCAAGACCTTGCCGAGAGATTTGACGTGTCCGTTTGCATCCTGGGCTCCCCTCGCTTTACCTGTGGCCGCCACTGCTGGGAGGTGGACGTGGGAACAAGCACAGAATGGGACCTGGGAGTCTGCAGAGAATCTGTTCACCGCAAAGGGAGGATCCAGCTGACCACAGAGCTTGGATTCTGGACTGTGAGTTTGAGGGATGGAGGCCGCCTCTCTGCCACCACGGTGCCGCTGACTTTCCTCTTCGTAGACCGCAAGTTACAGCGAGTGGGGATTTTTCTGGATATGGGCATGCAGAACGTTTCCTTTTTTGATGCTGAAAGTGGTTCCCATGTCTATACATTCAGGAGCGTATCTGCTGAGGAGCCATTGCGCCCATTTTTGGCTCCTTCAGTTCCACCTAATGGTGATCAAGGTGTCTTGAGCATCTGTCCTTTGATGAACTCAGGCACTACTGATGCTCCAGTCCGTCCTGGGGAGGC \n+\n+a score=6623803.0\n+s hg38.chr22 18627116 574 - 50818468 TGGATATGACCTTGGATGCCAACACAGCCAACAACTTCCTCCTCATTTCTGACGACCTCAGGAGCGTCCGAAGTGGGCGCATCAGACAGAATCGGCAAGACCTTGCCGAGAGATTTGACGTGTCCGTTTGCATCCTGGGCTCCCCTCGCTTTACCTGTGGCCGCCACTGCTGGGAGGTGGACGTGGGAACAAGCACAGAATGGGACCTGGGAGTCTGCAGAGAATCTGTTCACCGCAAAGGGAGGATCCAGCTGACCACAGAGCTTGGATTCTGGACTGTGAGTTTGAGGGATGGAGGCCGCCTCTCTGCCACCACGGTGCCGCTGACTTTCCTCTTCGTAGACCGCAAGTTACAGCGAGTGGGGATTTTTCTGGATATGGGCATGCAGAACGTTTCCTTTTTTGATGCTGAAAGTGGTTCCCATGTCTATACATTCAGGAGCGTATCTGCTGAGGAGCCATTGCGCCCATTTTTGGCTCCTTCAGTTCCACCTAATGGTGATCAAGGTGTCTTGAGCATCTGTCCTTTGATGAACTCAGGCACTACTGATGCTCCAGTCCGTCCTGGGGAGGC \n+\n+a score=6623803.0\n+s hg38.chr22 18627116 574 - 50818468 TGGATATGACCTTGGATGCCAACACAGCCAACAACTTCCTCCTCATTTCTGACGACCTCAGGAGCGTCCGAAGTGGGCGCATCAGACAGAATCGGCAAGACCTTGCCGAGAGATTTGACGTGTCCGTTTGCATCCTGGGCTCCCCTCGCTTTACCTGTGGCCGCCACTGCTGGGAGGTGGACGTGGGAACAAGCACAGAATGGGACCTGGGAGTCTGCAGAGAATCTGTTCACCGCAAAGGGAGGATCCAGCTGACCACAGAGCTTGGATTCTGGACTGTGAGTTTGAGGGATGGAGGCCGCCTCTCTGCCACCACGGTGCCGCTGACTTTCCTCTTCGTAGACCGCAAGTTACAGCGAGTGGGGATTTTTCTGGATATGGGCATGCAGAACGTTTCCTTTTTTGATGCTGAAAGTGGTTCCCATGTCTATACATTCAGGAGCGTATCTGCTGAGGAGCCATTGCGCCCATTTTTGGCTCCTTCAGTTCCACCTAATGGTGATCAAGGTGTCTTGAGCATCTGTCCTTTGATGAACTCAGGCACTACTGATGCTCCAGTCCGTCCTGGGGAGGC \n+\n+a score=6623803.0\n+s hg38.chr22 18627116 574 - 50818468 TGGATATGACCTTGGATGCCAACACAGCCAACAACTTCCTCCTCATTTCTGACGACCTCAGGAGCGTCCGAAGTGGGCGCATCAGACAGAATCGGCAAGACCTTGCCGAGAGATTTGACGTGTCCGTTTGCATCCTGGGCTCCCCTCGCTTTACCTGTGGCCGCCACTGCTGGGAGGTGGACGTGGGAACAAGCACAGAATGGGACCTGGGAGTCTGCAGAGAATCTGTTCACCGCAAAGGGAGGATCCAGCTGACCACAGAGCTTGGATTCTGGACTGTGAGTTTGAGGGATGGAGGCCGCCTCTCTGCCACCACGGTGCCGCTGACTTTCCTCTTCGTAGACCGCAAGTTACAGCGAGTGGGGATTTTTCTGGATATGGGCATGCAGAACGTTTCCTTTTTTGATGCTGAAAGTGGTTCCCATGTCTATACATTCAGGAGCGTATCTGCTGAGGAGCCATTGCGCCCATTTTTGGCTCCTTCAGTTCCACCTAATGGTGATCAAGGTGTCTTGAGCATCTGTCCTTTGATGAACTCAGGCACTACTGATGCTCCAGTCCGTCCTGGGGAGGC \n+\n+a score'..b'GCTGGGCCTGGTGCTGCTCGTGGAGGCCGTGGCCGTGCTCATCGGACCGCCCTCCGCCG \n+s mm10.chr15 24791713 98 - 104043685 GCTCATGGCAACCGTGGGTGCACCCCGCTTCCCTAGTGCATTGGGCCTAGTGCTGCTCGTGGAGGCCGTGGCTGTGCTCATAGGACCGCCCTCTGCCG \n+\n+a score=1184954.0\n+s hg38.chr22 12737495 36 - 50818468 CTCCTACGGCATGGTGGGCGCGCTGCAGTTCGAGGT \n+s eulFla1.LGHW01006107v1 634009 36 + 657376 CTCCTACGGCATGGTGGGCGCGCTGCAGTTCGAGGT \n+s mm10.chr15 24791677 36 - 104043685 GTCCTACGGCATGGTGGGCGCACTGCAGTTTGAGGT \n+\n+a score=4109169.0\n+s hg38.chr22 12737373 122 - 50818468 CTGCGGCCGCACGTCCCGTATCTGTTCAGCCTGGCCCTGCTGGCCAATGGGCTCACAGACCTGAGCAGCGCACGCGCGCGCTCCTACGGCGCCCTCGTCGCCTTCTGCGTCGCCTTCGGCCT \n+s eulFla1.LGHW01006107v1 633887 122 + 657376 CTGCGACCGCGGGTGCCCTATCTCTTCAGCCTGGCCCTGCTGGCCAACGGGCTCACGGACCTGAGCAGTGCGCGCGCGCGCTCCTACGGAGCCCTCGTCGCCTTCTGCATCGCCTTCGGCCT \n+s mm10.chr15 24791555 122 - 104043685 CTGAGACCCCACGTCCCCTACCTCTTCAGCCTGGCCCTGTTGGCCAATGGGCTCACGGACCTGATTAGCGCGCGTGCGCGCTCCTACGGGACCCTCGTTGCTTTCTGCATTGCCTTCGGCCT \n+\n+a score=8150994.0\n+s hg38.chr22 12737111 262 - 50818468 GCAGCTGCGCGAGGCATCCCCCAGGGTCCGGCCC--CGCCGGCGCCTGCTGGACTTGGCAGTGTGCACCGACCGCGCCTTCGCCGTGTACGCCGTCACCAAGTTCCTGATGGCGCTCGGGCTCTTCGTCCCCGCCATCCTGCTGGTGAACTACGCCAAGGACGCGGGCGTGCCCGACACCGACGCCGCCTTCCTGCTGTCCATCGTGGGCTTCGTGGACATCGTGGCGCGCCCGGCGTGCGGCGCCCTGGCGGGCCTGGCGCGT \n+s eulFla1.LGHW01006107v1 633625 262 + 657376 gcgcgtgcgcgaggcgCCCCCTGGCGGCCGCACC--CGCCGGCGGCTGCTGGACGTGGCTGTGTGTGCCGACCGCGCCTTCGTGGTGTACGCGGTCACCAAGTTCCTGATGGCGCTCGGGCTCTTCGTGCCCGCCATCCTGCTGGTGAACTACGCCAAGGACGCGGGCGTGCCTGACGCCGACGCCGCCTTCCTGTTATCCATCGTGGGCTTCGTAGACATCGTGGCGCGGCCAGCGTGCGGCGCCCTGGCGGGCCTGGCGCGC \n+s mm10.chr15 24791316 239 - 104043685 -------------------------GCCCGGCTCGCCGCCGGCGGCTGCTGGACGTGGCAGTGTGCACCGACCGTGCTTTCGTGGTGTACGTGGTCACCAAGTTCCTGATGGCACTCGGGCTCTTTGTGCCGGCCATCCTGCTGGTGAACTACGCCAAGGACGCGGGCGTGCCTGACGCCGAGGCCGCCTTCTTGCTGTCCATCGTGGGCTTCGTGGACATCGTGGCACGACCGGCGTGCGGTGCTTTGGCGGGTCTGGGGCGC \n+\n+a score=373719.0\n+s hg38.chr22 12737090 21 - 50818468 GGAGGCTGACGGTGCGGGGCT \n+s eulFla1.LGHW01006107v1 633604 21 + 657376 ggaggcggagggcgaggggct \n+s mm10.chr15 24791310 6 - 104043685 --------ACGGTG------- \n+\n+a score=149374.0\n+s hg38.chr22 12737084 6 - 50818468 CGAGGC \n+s eulFla1.LGHW01006107v1 633592 6 + 657376 Agaggc \n+\n+a score=172154.0\n+s hg38.chr22 12737070 14 - 50818468 GGGGACGCTCCGGG \n+s eulFla1.LGHW01006107v1 633578 14 + 657376 ggggACTCTGCGGG \n+s mm10.chr15 24791305 5 - 104043685 ------GCCCC--- \n+\n+a score=5393236.0\n+s hg38.chr22 12736861 209 - 50818468 TGGCCAACGGGCTGGCGGCGGCGGGCAGCCCCGTGTTCCTGTCCGCGCTGTCGCCGCTCGGCCAGCAGCTGCTGGAGCGCTTCGGCTGGCGCGGCGGCTTCCTGCTGCTCGGCGGGCTCCTGCTGCACTGCTGCGCCTGCGGGGCTGTCATGAGGCCGCCGCCCGGGCCGGGCCCGCGACCG------CGCAGGGACAGCGCCGGCGACCGCGCC \n+s eulFla1.LGHW01006107v1 633363 215 + 657376 TGGCCAACGGGCTGGCGGCGGCGGGCAGCCCCGTGTTCCTGTCCGTGCTGTCGCCTCTCGGCCAGCAGCTGCTCGAGCACTTCGGCTGGCGCGGCGGCTTCCTGCTGCTCGGCGGGCTCCTGCTGCACTGCTGCGCGTGCGGAGCCGTCATGCggccgccgccggggccggggccggggccaccgccgcgcggggccggcgcccgggacctggcg \n+s mm10.chr15 24791115 190 - 104043685 TGGCCAACGGGCTGGCAGCGGCGGGCAGTCCCGTGTTTCTGTCCATGCTGTCGCCGCTCGGGCAGCTGCTGGGGGAGCGCTTCGGCTGGCGTGGCGGCTTCCTGCTGTTTGGCGGCCTCCTGCTGCACTGTTGCGCCTGTGGGGCAGTCATGCGTCCGCCCCCTGGACC---CCCG---CCG------CGCAGAGACCCCTC------------- \n+\n+a score=810987.0\n+s hg38.chr22 12736835 26 - 50818468 GCTGTACTTCGAGCGGCGGCGGCCTC \n+s eulFla1.LGHW01006107v1 633337 26 + 657376 GCTGTACTTCGAGCGGCGGCGGCCTC \n+s mm10.chr15 24791089 26 - 104043685 ACTCTACTTCGAGCGGCGACGGCCCC \n+\n+a score=2187734.0\n+s hg38.chr22 12736789 46 - 50818468 GCCTGGGCCTGGCCCTCAACTTCCAGCCGTCGCTCATCATGCTGGG \n+s eulFla1.LGHW01006107v1 633291 46 + 657376 GCCTGGGCCTGGCCCTCAACTTCCAGCCGTCGCTCATCATGCTGGG \n+s mm10.chr15 24791043 46 - 104043685 GCCTGGGCCTAGCTCTCAACTTCCAGCCGTCGCTCATCATGCTGGG \n+\n' |
| b |
| diff -r 000000000000 -r cfea1d6354db test-data/local/interval2maf-in1-1.maf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/local/interval2maf-in1-1.maf Fri Jul 17 10:56:42 2020 -0400 |
| b |
| b'@@ -0,0 +1,1652 @@\n+##maf version=1\n+a score=5126687.0\n+s hg38.chr22 33698927 151 - 50818468 GGCCAGAGGGGGCTACGGTGCTCCGCCCTCCGCCCCTCCACCACCTCCGCCACCACC---TCAGGGAGGCTCCCAGCTGGGCCACTGCATCTCGGAGAACGAGGGGGGTGCTCATGGCTATGTCAACACCCTGGCTGTGGCCTCTCAGAATTGA \n+s eulFla1.LGHW01008773v1 48579 151 - 91162 GGCCAGAGCGGGTTACGGcgccccgccctccgccccgccgccacctccgcctccacc---tcAGGGAGGCTCCCAGCTGGGCCACTGCATCTCGGAGAACGAGGGGGGCGCCCACGGCTATGTCAACACTCTGGCGGTGGCCTCCCAGAATTGA \n+s mm10.chr6 29244363 148 - 149736546 GGCCAGAAGCAGCTATGGTGCTCCTCCCTCTGCCCCTCCCCCACCTCCACCACCACCACCTCAGGGAGGCTCCCAGCGGGGCCACT------TGGAAAATGAAGGGGGCCCTCATGGCTATGTCAACACTCTAGCTGTTGCCTCTCAGAATTGA \n+\n+a score=3181394.0\n+s hg38.chr22 33698828 99 - 50818468 CTCCATCTTCATGCTCAAGAACCTCTTCTTCCTCGGCTGCCGGGGCCTGGAGGCCCTGGAGGGCTGCTGGGACCGGGGCAATCGGGCCTCCCCGAGTCG \n+s eulFla1.LGHW01008773v1 48480 99 - 91162 CTCCGTCTTCATGCTCAAGAACCTCTTCTTCCTTGGCTGCCGCGGCCTGGAGGCCCTGGAGGGCTGCTGGGACCGGGGCGGCCGGGCCTCCCCTAGTCG \n+s mm10.chr6 29244264 99 - 149736546 GTCCATCTTTATGCTCAAGAATCTCTTTTTCCTTGGCTGCCGTGGCCTGGAGGCCTTGGAGGGCTGCTGGGACCGGGGGAGTTGGGTATCCCCAAGTCG \n+\n+a score=8321735.0\n+s hg38.chr22 33698587 241 - 50818468 GCCGCGTGCCGCTGCCCGCGCACCTGCGCTACCTGCTTATCGCCGTCTACTTCCTCACCCTCGCCTCGCCGGTGCTCTGGCTCTACGAGCTCAACGCCGCGGCCGCAGCGGCTGCATCCTGGGGCCAGGCCTCCGGGCCTGGCAGCTGCAGCCGCCTTCTGCGCCTGCTGGGCGGCTGCCTGGTGGACGTGCCCTTGCTGGCGCTGCGCTGCCTCCTGGTGGTCAGCTACCAGCAGCCCCT \n+s eulFla1.LGHW01008773v1 48254 226 - 91162 GCCGCGTGCCGCTGCCCGCGCACCTGCGCTACCTGCTCATCGCCGTCTACTTCCTCACGCTCGCCTCGCCGGTGCTCTGGCTCTACGAACTCAACGCC---------------TCGTCCTGGGGCCAGGCCTCGGGGCCCGGCAGCTGCAGCCGCCTCCTGCGCCTGCTGGGCGGCTGCCTGGTGGACGTGCCCTTGCTGGCCCTGCGCTGCCTCCTAGTGGTGAGCTACCAGCAGCCCCT \n+s mm10.chr6 29244026 238 - 149736546 GCCGCGTGCCGCTTCCGGCGCACCTGCGCTACCTGCTCATCGCCGTCTACTTCCTCACTCTTGCCTCCCCAGTGCTCTGGCTGTACGAGCTGAACACT---GCCACAGCAGCTCCGTCCTGGGGTCAGACCTCCGGGCCCGGAAGCTGCAGCCGCCTTTTACGTTTGCTGGGCGGCTGCCTGGTGGACGTGCCCTTGCTGGCGCTGCGCAGCCTCCTGGTCGTGAGCTACCAACAGCCGCT \n+\n+a score=3395583.0\n+s hg38.chr22 33698483 104 - 50818468 ACCCCTGCTGCTGCAGCCCCAGCGGCACCGCGCGGCCGGATGCTTCCTGGGCACGTGCTTGGACCTGCTCGACAGCTTCACGCTGGTGGAGCTGATGCTGGAGG \n+s eulFla1.LGHW01008773v1 48150 104 - 91162 ACCCCTGCTGCTGCAGCCCCAGCGGCACCGCGCCGCCGGCTGCTTCCTGGGCACGTGTCTGGACCTGCTCGACAGCTTCACCCTGGTGGAGCTGACGCTGGAAG \n+s mm10.chr6 29243922 104 - 149736546 TCCCCTGCTCCTGCAGCCACAGCAGCATCGCGCCGCGGGCTGCTTCCTGGGCACGTGTCTGGACCTGCTGGACAGCTTTACACTGGTGGAGCTGATGCTGGACG \n+\n+a score=2062525.0\n+s hg38.chr22 33698413 70 - 50818468 TGTCGGTGCCCCTGCTCTACAGCTTGGTGCGGGCCATCAGCGAGGCGGGCGCGCCCCCGGGATCGGCAGG \n+s eulFla1.LGHW01008773v1 48080 70 - 91162 TGTCGGTGCCCCTGCTCTACAGCTTGGTGCGGGCCATCAGCGAGGCGGGCGCCCCGCCGGGCTCTGCGGG \n+s mm10.chr6 29243852 70 - 149736546 TGTCCGTGCCGCTGCTCTACAGCCTAGTGCGTGCCATTAGCGAGGCGGGCGCGCCCCCGGGCTCGGCGGG \n+\n+a score=4187755.0\n+s hg38.chr22 33698268 145 - 50818468 GAGTTCGCCTTCGCCTACCTGGCCTGGCTTATCTACTCCATCGCCTTCACTCCCAAGGTGGTGCTGATCCTGGGCACGTCCATCCTAGACCTCATCGAGCTACGCGCGCCCTTCGGCACCACGGGCTTCCGTCTCACCATGGCGC \n+s eulFla1.LGHW01008773v1 47935 145 - 91162 GAGTTCGCCTTCGCCTACCTGGCCTGGCTCATCTACTCCATCGCCTTCACGCCCAAGGTGGTGCTTATCCTGGGCACGTCCATCCTGGACCTCATCGAGCTGCGCGCGCCCTTCGGCACCACCGGCTTCCGCCTCACCATGGCGC \n+s mm10.chr6 29243707 145 - 149736546 GAGTTCGCTTTTGCGTACCTGGCCTGGCTCATCTACTCCATCGCTTTCACCCCTAAGGTGGTGCTCATCCTGGGCACATCCATCCTGGACCTCATCGAGCTGCGCGCGCCCTTTGGCACCACGGGCTTTCGCCTTACCATGGCGC \n+\n+a score=491529.0\n+s hg38.chr22 33698246 22 - 50818468 GGGGGCGGCCGCGGCAGCGGGC \n+s eulFla1.LGHW01008773v1 47913 22 - 91162 GGCGGCGGCCGGGGCAACCGGC \n+s mm10.chr6 29243685 22 - 149736546 GGGGACGACTGGGGCAGCGGGC \n+\n+a score=17457.0\n+s hg38.chr22 33698245 1 - 50818468 T \n+s eulFla1.LGHW01008773v1 47912 1 - 91162 T \n+s mm10.chr6 29243684 1 - 149736546 C \n+\n+a score=263332.0\n+s hg38.chr22 '..b'TTTGAGCTAGAACAGAACATCAAAGAACTTAACACCCTTGCGGACCAAGTTGACACCACTCACGAGTTGCTTACCAAGACCAGCCTGGTGGCCAGCTCTTCCGGGGCTGTTTCTGGGGTCATGAACATCCTGGGTTTGGCCCTAGCACCTGTGACAGCAGGAGGCAGTCTCATGCTCTCAGCAACTGGGACAGGGTTGGGGGCAGCAGCTG \n+s eulFla1.LGHW01001967v1 331301 239 + 548553 GTTTCTGTCCTATTTTCCCTTGAAGAAGTATCAGCTGGAAAAGAATATCCGAGAACTCAACACCATTGCAGACCAAGTTGATATGACCCACAGGAAGCTCACCAAGGCCAGCCTGGTGGCCAGCTCTTCGGGGGCTGTTTCTGGAGTCATGAGCATCCTGGGTTTTGCCCTGGCACCTGTGACAGTAGGAGGCAGTCTCGTGCTCTCAGCAGCTGGGGTGGGGTTGGGGGCAGCAGCTG \n+i eulFla1.LGHW01001967v1 C 0 C 0 \n+\n+a score=372641.0\n+s hg38.chr22 35726609 13 + 50818468 CCATCACCAACAT \n+s eulFla1.LGHW01001967v1 331540 13 + 548553 CCATCACCAAGGT \n+i eulFla1.LGHW01001967v1 C 0 C 0 \n+\n+a score=572286.0\n+s hg38.chr22 35726622 28 + 50818468 AGTAACAAATGTCTTAGAAAATAGAAGC \n+s eulFla1.LGHW01001967v1 331553 28 + 548553 TTTGACAAATGCCTTAGAAAATAGAAGC \n+i eulFla1.LGHW01001967v1 C 0 C 0 \n+\n+a score=904228.0\n+s hg38.chr22 35726650 36 + 50818468 AATTCAGCAGCAAGAGACAAAGCCAGCCGACTGGGG \n+s eulFla1.LGHW01001967v1 331581 36 + 548553 AATTCAGCAGCAAGAGACAAAGCTAGCAGACTGGTG \n+i eulFla1.LGHW01001967v1 C 0 I 20 \n+\n+a score=55358.0\n+s hg38.chr22 35726686 3 + 50818468 CCT \n+\n+a score=139942.0\n+s hg38.chr22 35726689 11 + 50818468 CTGACAACATC \n+\n+a score=1764916.0\n+s hg38.chr22 35726700 97 + 50818468 A-CATGAGGCTTTCGGAGGAATAAATTGGTCTGAAATCGAGGCTGCTGGCTTTTGTGTTAATAAGTGTGTAAAAGCTATCCAGGGCATCAAGGATCTT \n+s eulFla1.LGHW01001967v1 331637 88 + 548553 -GCATGAGGCTTTCGGAGGAATAAAGTTGCCTGAAGGTGAGGCTGCTGGCCAGTGTGTTGGTAAGTGTATAAGCATCATCAAGAGTCTT--------- \n+i eulFla1.LGHW01001967v1 I 20 C 0 \n+\n+a score=4155522.0\n+s hg38.chr22 35726797 189 + 50818468 CATGCCTACCAGATGGCCAAATCCAACTCTGGCTTCATGGCTATGGTCAAGAATTTTGTGGCCAAGAGACACATCCCTTTCTGGACGGCTAGAGGGGTGCAGAGAGCCTTTGAGGGCACAACTCTGGCCATGACCAATGGTGCCTGGGTGATGGGTGCTGCTGGGGCTGGCTTCTTACTTATGAAAGAC \n+s eulFla1.LGHW01001967v1 331725 189 + 548553 CGTGCCCACCAGATGGCCAAAGCTAACCTTGGCTTCATGGCTATGGTCAAGAATTTTGTGGCCACACACAACATCTCTTTCTGGAAGCCAGGAGAGGTGCAGACAATCTTTGTAGATGCAACTCTGGCGGTGACCAAGGGTGCCCAGGGGATGGGTGCTGCTGGGGCTGGCCTCTTTCTTATGCAAGAT \n+i eulFla1.LGHW01001967v1 C 0 C 0 \n+\n+a score=10960.0\n+s hg38.chr22 35726986 1 + 50818468 A \n+s eulFla1.LGHW01001967v1 331914 1 + 548553 G \n+i eulFla1.LGHW01001967v1 C 0 C 0 \n+\n+a score=2757722.0\n+s hg38.chr22 35726987 103 + 50818468 TGAGCAGCTTCCTGCAGAGCTGGAAGCACCTGGAGGATGGGGCAAGGACGGAGACAGCAGAGGAACTGAGAGCACTTGCTAAGAAGCTGGAGCAGGAGCTGGA \n+s eulFla1.LGHW01001967v1 331915 103 + 548553 TGGGCAAACTTCTGCAGAACTGGAAGCACCTGGAGGAGGGGGCGAGGGCAGAGACAGCCAAGGAACTGAGGACACTTGCCAAGGAGCAGGAGCAGGAGCTGAG \n+i eulFla1.LGHW01001967v1 C 0 C 0 \n+\n+a score=841012.0\n+s hg38.chr22 35727090 49 + 50818468 CCGGCTCACCCAGCACCACCGGCACCTGCCGCAGAAGGCGAGCCAGACC \n+s eulFla1.LGHW01001967v1 332018 49 + 548553 GCAGCTCGCCGAGCGCTACCAGGACCTGCAGCAGAAGGCGAGCCAGACC \n+i eulFla1.LGHW01001967v1 C 0 I 915 \n+\n+a score=668337.0\n+s hg38.chr22 35727139 55 + 50818468 TGTTCCAGCTCCCGGGGCAGGGCTGTTCGAGGATCCCGTGTGGTTAAACCAGAAG \n+\n' |
| b |
| diff -r 000000000000 -r cfea1d6354db test-data/local/interval2maf-in1-1.maf.index |
| b |
| Binary file test-data/local/interval2maf-in1-1.maf.index has changed |
| b |
| diff -r 000000000000 -r cfea1d6354db test-data/local/interval2maf-in1-2.maf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/local/interval2maf-in1-2.maf Fri Jul 17 10:56:42 2020 -0400 |
| b |
| b'@@ -0,0 +1,2623 @@\n+##maf version=1\n+a score=196573.0\n+s hg38.chr22 18627690 7 - 50818468 CAAATAA \n+\n+a score=6623803.0\n+s hg38.chr22 18627116 574 - 50818468 TGGATATGACCTTGGATGCCAACACAGCCAACAACTTCCTCCTCATTTCTGACGACCTCAGGAGCGTCCGAAGTGGGCGCATCAGACAGAATCGGCAAGACCTTGCCGAGAGATTTGACGTGTCCGTTTGCATCCTGGGCTCCCCTCGCTTTACCTGTGGCCGCCACTGCTGGGAGGTGGACGTGGGAACAAGCACAGAATGGGACCTGGGAGTCTGCAGAGAATCTGTTCACCGCAAAGGGAGGATCCAGCTGACCACAGAGCTTGGATTCTGGACTGTGAGTTTGAGGGATGGAGGCCGCCTCTCTGCCACCACGGTGCCGCTGACTTTCCTCTTCGTAGACCGCAAGTTACAGCGAGTGGGGATTTTTCTGGATATGGGCATGCAGAACGTTTCCTTTTTTGATGCTGAAAGTGGTTCCCATGTCTATACATTCAGGAGCGTATCTGCTGAGGAGCCATTGCGCCCATTTTTGGCTCCTTCAGTTCCACCTAATGGTGATCAAGGTGTCTTGAGCATCTGTCCTTTGATGAACTCAGGCACTACTGATGCTCCAGTCCGTCCTGGGGAGGC \n+\n+a score=196573.0\n+s hg38.chr22 18627690 7 - 50818468 CAAATAA \n+\n+a score=6623803.0\n+s hg38.chr22 18627116 574 - 50818468 TGGATATGACCTTGGATGCCAACACAGCCAACAACTTCCTCCTCATTTCTGACGACCTCAGGAGCGTCCGAAGTGGGCGCATCAGACAGAATCGGCAAGACCTTGCCGAGAGATTTGACGTGTCCGTTTGCATCCTGGGCTCCCCTCGCTTTACCTGTGGCCGCCACTGCTGGGAGGTGGACGTGGGAACAAGCACAGAATGGGACCTGGGAGTCTGCAGAGAATCTGTTCACCGCAAAGGGAGGATCCAGCTGACCACAGAGCTTGGATTCTGGACTGTGAGTTTGAGGGATGGAGGCCGCCTCTCTGCCACCACGGTGCCGCTGACTTTCCTCTTCGTAGACCGCAAGTTACAGCGAGTGGGGATTTTTCTGGATATGGGCATGCAGAACGTTTCCTTTTTTGATGCTGAAAGTGGTTCCCATGTCTATACATTCAGGAGCGTATCTGCTGAGGAGCCATTGCGCCCATTTTTGGCTCCTTCAGTTCCACCTAATGGTGATCAAGGTGTCTTGAGCATCTGTCCTTTGATGAACTCAGGCACTACTGATGCTCCAGTCCGTCCTGGGGAGGC \n+\n+a score=196573.0\n+s hg38.chr22 18627690 7 - 50818468 CAAATAA \n+\n+a score=6623803.0\n+s hg38.chr22 18627116 574 - 50818468 TGGATATGACCTTGGATGCCAACACAGCCAACAACTTCCTCCTCATTTCTGACGACCTCAGGAGCGTCCGAAGTGGGCGCATCAGACAGAATCGGCAAGACCTTGCCGAGAGATTTGACGTGTCCGTTTGCATCCTGGGCTCCCCTCGCTTTACCTGTGGCCGCCACTGCTGGGAGGTGGACGTGGGAACAAGCACAGAATGGGACCTGGGAGTCTGCAGAGAATCTGTTCACCGCAAAGGGAGGATCCAGCTGACCACAGAGCTTGGATTCTGGACTGTGAGTTTGAGGGATGGAGGCCGCCTCTCTGCCACCACGGTGCCGCTGACTTTCCTCTTCGTAGACCGCAAGTTACAGCGAGTGGGGATTTTTCTGGATATGGGCATGCAGAACGTTTCCTTTTTTGATGCTGAAAGTGGTTCCCATGTCTATACATTCAGGAGCGTATCTGCTGAGGAGCCATTGCGCCCATTTTTGGCTCCTTCAGTTCCACCTAATGGTGATCAAGGTGTCTTGAGCATCTGTCCTTTGATGAACTCAGGCACTACTGATGCTCCAGTCCGTCCTGGGGAGGC \n+\n+a score=196573.0\n+s hg38.chr22 18627690 7 - 50818468 CAAATAA \n+\n+a score=6623803.0\n+s hg38.chr22 18627116 574 - 50818468 TGGATATGACCTTGGATGCCAACACAGCCAACAACTTCCTCCTCATTTCTGACGACCTCAGGAGCGTCCGAAGTGGGCGCATCAGACAGAATCGGCAAGACCTTGCCGAGAGATTTGACGTGTCCGTTTGCATCCTGGGCTCCCCTCGCTTTACCTGTGGCCGCCACTGCTGGGAGGTGGACGTGGGAACAAGCACAGAATGGGACCTGGGAGTCTGCAGAGAATCTGTTCACCGCAAAGGGAGGATCCAGCTGACCACAGAGCTTGGATTCTGGACTGTGAGTTTGAGGGATGGAGGCCGCCTCTCTGCCACCACGGTGCCGCTGACTTTCCTCTTCGTAGACCGCAAGTTACAGCGAGTGGGGATTTTTCTGGATATGGGCATGCAGAACGTTTCCTTTTTTGATGCTGAAAGTGGTTCCCATGTCTATACATTCAGGAGCGTATCTGCTGAGGAGCCATTGCGCCCATTTTTGGCTCCTTCAGTTCCACCTAATGGTGATCAAGGTGTCTTGAGCATCTGTCCTTTGATGAACTCAGGCACTACTGATGCTCCAGTCCGTCCTGGGGAGGC \n+\n+a score=196573.0\n+s hg38.chr22 18627690 7 - 50818468 CAAATAA \n+\n+a score=6623803.0\n+s hg38.chr22 18627116 574 - 50818468 TGGATATGACCTTGGATGCCAACACAGCCAACAACTTCCTCCTCATTTCTGACGACCTCAGGAGCGTCCGAAGTGGGCGCATCAGACAGAATCGGCAAGACCTTGCCGAGAGATTTGACGTGTCCGTTTGCATCCTGGGCTCCCCTCGCTTTACCTGTGGCCGCCACTGCTGGGAGGTGGACGTGGGAACAAGCACAGAATGGGACCTGGGAGTCTGCAGAGAATCTGTTCACCGCAAAGGGAGGATCCAGCTGACCACAGAGCTTGGATTCTGGACTGTGAGTTTGAGGGATGGAGGCCGCCTCTCTGCCACCACGGTGCCGCTGACTTTCCTCTTCGTAGACCGCAAGTTACAGCGAGTGGGGATTTTTCTGGATATGGGCATGCAGAACGTTTCCTTTTTTGATGCTGAAAGTGGTTCCCATGTCTATACATTCAGGAGCGTATCTGCTGAGGAGCCATTGCGCCCATTTTTGGCTCCTTCAGTTCCACCTAATGGTGATCAAGGTGTCTTGAGCATCTGTCCTTTGATGAACTCAGGCACTACTGATGCTCCAGTCCGTCCTGGGGAGGC \n+\n+a score=222067.0\n+s hg38.chr22 32358071 23 + 50818468 ATGAAAAGGTTGTCACTTGTCAC \n+\n+a score=28783.0\n+s hg38.chr22 32358094 6 + 50818468 AACTAA \n+\n+a score=94379.0\n+s hg38.chr22 32358100 18 + 50818468 CAGGCTTTCACCTCAAGG \n+\n+a score=12732.0\n+s hg38.chr22 32358118 2 + 50818468 AA \n+\n+a score=325051.0\n+s hg38.chr22 32358120 57 + 50818468 ATTTTCTTCCCTTGTGTACTTTTCCCCTGGCAGTGGACATGGCTGCACTCTTCCAAG \n+\n+a score=2523686.0\n+s hg38.chr22 32358177 267 + 50818468 AAGCAAGCAG'..b'GCTGGGCCTGGTGCTGCTCGTGGAGGCCGTGGCCGTGCTCATCGGACCGCCCTCCGCCG \n+s mm10.chr15 24791713 98 - 104043685 GCTCATGGCAACCGTGGGTGCACCCCGCTTCCCTAGTGCATTGGGCCTAGTGCTGCTCGTGGAGGCCGTGGCTGTGCTCATAGGACCGCCCTCTGCCG \n+\n+a score=1184954.0\n+s hg38.chr22 12737495 36 - 50818468 CTCCTACGGCATGGTGGGCGCGCTGCAGTTCGAGGT \n+s eulFla1.LGHW01006107v1 634009 36 + 657376 CTCCTACGGCATGGTGGGCGCGCTGCAGTTCGAGGT \n+s mm10.chr15 24791677 36 - 104043685 GTCCTACGGCATGGTGGGCGCACTGCAGTTTGAGGT \n+\n+a score=4109169.0\n+s hg38.chr22 12737373 122 - 50818468 CTGCGGCCGCACGTCCCGTATCTGTTCAGCCTGGCCCTGCTGGCCAATGGGCTCACAGACCTGAGCAGCGCACGCGCGCGCTCCTACGGCGCCCTCGTCGCCTTCTGCGTCGCCTTCGGCCT \n+s eulFla1.LGHW01006107v1 633887 122 + 657376 CTGCGACCGCGGGTGCCCTATCTCTTCAGCCTGGCCCTGCTGGCCAACGGGCTCACGGACCTGAGCAGTGCGCGCGCGCGCTCCTACGGAGCCCTCGTCGCCTTCTGCATCGCCTTCGGCCT \n+s mm10.chr15 24791555 122 - 104043685 CTGAGACCCCACGTCCCCTACCTCTTCAGCCTGGCCCTGTTGGCCAATGGGCTCACGGACCTGATTAGCGCGCGTGCGCGCTCCTACGGGACCCTCGTTGCTTTCTGCATTGCCTTCGGCCT \n+\n+a score=8150994.0\n+s hg38.chr22 12737111 262 - 50818468 GCAGCTGCGCGAGGCATCCCCCAGGGTCCGGCCC--CGCCGGCGCCTGCTGGACTTGGCAGTGTGCACCGACCGCGCCTTCGCCGTGTACGCCGTCACCAAGTTCCTGATGGCGCTCGGGCTCTTCGTCCCCGCCATCCTGCTGGTGAACTACGCCAAGGACGCGGGCGTGCCCGACACCGACGCCGCCTTCCTGCTGTCCATCGTGGGCTTCGTGGACATCGTGGCGCGCCCGGCGTGCGGCGCCCTGGCGGGCCTGGCGCGT \n+s eulFla1.LGHW01006107v1 633625 262 + 657376 gcgcgtgcgcgaggcgCCCCCTGGCGGCCGCACC--CGCCGGCGGCTGCTGGACGTGGCTGTGTGTGCCGACCGCGCCTTCGTGGTGTACGCGGTCACCAAGTTCCTGATGGCGCTCGGGCTCTTCGTGCCCGCCATCCTGCTGGTGAACTACGCCAAGGACGCGGGCGTGCCTGACGCCGACGCCGCCTTCCTGTTATCCATCGTGGGCTTCGTAGACATCGTGGCGCGGCCAGCGTGCGGCGCCCTGGCGGGCCTGGCGCGC \n+s mm10.chr15 24791316 239 - 104043685 -------------------------GCCCGGCTCGCCGCCGGCGGCTGCTGGACGTGGCAGTGTGCACCGACCGTGCTTTCGTGGTGTACGTGGTCACCAAGTTCCTGATGGCACTCGGGCTCTTTGTGCCGGCCATCCTGCTGGTGAACTACGCCAAGGACGCGGGCGTGCCTGACGCCGAGGCCGCCTTCTTGCTGTCCATCGTGGGCTTCGTGGACATCGTGGCACGACCGGCGTGCGGTGCTTTGGCGGGTCTGGGGCGC \n+\n+a score=373719.0\n+s hg38.chr22 12737090 21 - 50818468 GGAGGCTGACGGTGCGGGGCT \n+s eulFla1.LGHW01006107v1 633604 21 + 657376 ggaggcggagggcgaggggct \n+s mm10.chr15 24791310 6 - 104043685 --------ACGGTG------- \n+\n+a score=149374.0\n+s hg38.chr22 12737084 6 - 50818468 CGAGGC \n+s eulFla1.LGHW01006107v1 633592 6 + 657376 Agaggc \n+\n+a score=172154.0\n+s hg38.chr22 12737070 14 - 50818468 GGGGACGCTCCGGG \n+s eulFla1.LGHW01006107v1 633578 14 + 657376 ggggACTCTGCGGG \n+s mm10.chr15 24791305 5 - 104043685 ------GCCCC--- \n+\n+a score=5393236.0\n+s hg38.chr22 12736861 209 - 50818468 TGGCCAACGGGCTGGCGGCGGCGGGCAGCCCCGTGTTCCTGTCCGCGCTGTCGCCGCTCGGCCAGCAGCTGCTGGAGCGCTTCGGCTGGCGCGGCGGCTTCCTGCTGCTCGGCGGGCTCCTGCTGCACTGCTGCGCCTGCGGGGCTGTCATGAGGCCGCCGCCCGGGCCGGGCCCGCGACCG------CGCAGGGACAGCGCCGGCGACCGCGCC \n+s eulFla1.LGHW01006107v1 633363 215 + 657376 TGGCCAACGGGCTGGCGGCGGCGGGCAGCCCCGTGTTCCTGTCCGTGCTGTCGCCTCTCGGCCAGCAGCTGCTCGAGCACTTCGGCTGGCGCGGCGGCTTCCTGCTGCTCGGCGGGCTCCTGCTGCACTGCTGCGCGTGCGGAGCCGTCATGCggccgccgccggggccggggccggggccaccgccgcgcggggccggcgcccgggacctggcg \n+s mm10.chr15 24791115 190 - 104043685 TGGCCAACGGGCTGGCAGCGGCGGGCAGTCCCGTGTTTCTGTCCATGCTGTCGCCGCTCGGGCAGCTGCTGGGGGAGCGCTTCGGCTGGCGTGGCGGCTTCCTGCTGTTTGGCGGCCTCCTGCTGCACTGTTGCGCCTGTGGGGCAGTCATGCGTCCGCCCCCTGGACC---CCCG---CCG------CGCAGAGACCCCTC------------- \n+\n+a score=810987.0\n+s hg38.chr22 12736835 26 - 50818468 GCTGTACTTCGAGCGGCGGCGGCCTC \n+s eulFla1.LGHW01006107v1 633337 26 + 657376 GCTGTACTTCGAGCGGCGGCGGCCTC \n+s mm10.chr15 24791089 26 - 104043685 ACTCTACTTCGAGCGGCGACGGCCCC \n+\n+a score=2187734.0\n+s hg38.chr22 12736789 46 - 50818468 GCCTGGGCCTGGCCCTCAACTTCCAGCCGTCGCTCATCATGCTGGG \n+s eulFla1.LGHW01006107v1 633291 46 + 657376 GCCTGGGCCTGGCCCTCAACTTCCAGCCGTCGCTCATCATGCTGGG \n+s mm10.chr15 24791043 46 - 104043685 GCCTGGGCCTAGCTCTCAACTTCCAGCCGTCGCTCATCATGCTGGG \n+\n' |
| b |
| diff -r 000000000000 -r cfea1d6354db test-data/local/interval2maf-in1-2.maf.index |
| b |
| Binary file test-data/local/interval2maf-in1-2.maf.index has changed |
| b |
| diff -r 000000000000 -r cfea1d6354db test-data/local/maf_indexes.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/local/maf_indexes.loc Fri Jul 17 10:56:42 2020 -0400 |
| b |
| @@ -0,0 +1,7 @@ +#This is a sample file distributed with Galaxy that is used by some +#alignment tools. The maf_index.loc file has this format (white space +#characters are TAB characters): +# +#<Display_name UID> <indexed_for:build1,build2,build3> <exists_in_maf:build1,build2,build3> <Comma_Separated_List_of_Full_Paths_To_Files> +# +Test TEST hg38,eulFla1,mm10 hg38,eulFla1,mm10 ${__HERE__}/interval2maf-in1-1.maf,${__HERE__}/interval2maf-in1-2.maf |
| b |
| diff -r 000000000000 -r cfea1d6354db tool-data/maf_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/maf_indexes.loc.sample Fri Jul 17 10:56:42 2020 -0400 |
| b |
| b'@@ -0,0 +1,17 @@\n+#This is a sample file distributed with Galaxy that is used by some\n+#alignment tools. The maf_index.loc file has this format (white space \n+#characters are TAB characters):\n+#\n+#<Display_name UID>\t<indexed_for:build1,build2,build3>\t<exists_in_maf:build1,build2,build3>\t<Comma_Separated_List_of_Full_Paths_To_Files>\n+#\n+#ENCODE TBA (hg17)\tENCODE_TBA_hg17\tarmadillo,baboon,galGal2,panTro1,colobus_monkey,cow,canFam1,dusky_titi,elephant,fr1,galago,hedgehog,hg17,rheMac1,marmoset,monDom1,mm6,mouse_lemur,owl_monkey,platypus,rabbit,rn3,rfbat,shrew,tenrec,tetNig1,xenTro1,danRer2\tarmadillo,baboon,galGal2,panTro1,colobus_monkey,cow,canFam1,dusky_titi,elephant,fr1,galago,hedgehog,hg17,rheMac1,marmoset,monDom1,mm6,mouse_lemur,owl_monkey,platypus,rabbit,rn3,rfbat,shrew,tenrec,tetNig1,xenTro1,danRer2\t/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm001/human.ENm001.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm002/human.ENm002.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm003/human.ENm003.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm004/human.ENm004.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm005/human.ENm005.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm006/human.ENm006.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm007/human.ENm007.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm008/human.ENm008.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm009/human.ENm009.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm010/human.ENm010.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm011/human.ENm011.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm012/human.ENm012.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm013/human.ENm013.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm014/human.ENm014.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr111/human.ENr111.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr112/human.ENr112.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr113/human.ENr113.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr114/human.ENr114.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr121/human.ENr121.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr122/human.ENr122.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr123/human.ENr123.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr131/human.ENr131.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr132/human.ENr132.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr133/human.ENr133.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr211/human.ENr211.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr212/human.ENr212.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr213/human.ENr213.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr221/human.ENr221.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr222/human.ENr222.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr223/human.ENr223.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr231/human.ENr231.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr232/human.ENr232.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr233/human.ENr233.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr311/human.ENr311.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr312/human.ENr312.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr313/human.ENr313.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr321/human.ENr321.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr322/human.ENr322.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr323/human.ENr323.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr324/human.ENr324.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr331/human.ENr331.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr332/human.ENr3'..b'data2/galaxy/mm8/align/multiz17way/chrX_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chrY.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chrY_random.maf.lzo\n+#8-way multiZ (ponAbe2)\t8_WAY_MULTIZ_ponAbe2\tponAbe2,hg18,panTro2,rheMac2,calJac1,mm9,monDom4,ornAna1\tponAbe2,hg18,panTro2,rheMac2,calJac1,mm9,monDom4,ornAna1\t/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr10.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr10_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr11.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr11_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr12.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr12_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr13.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr13_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr14.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr14_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr15.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr15_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr16.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr16_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr17.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr17_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr18.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr18_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr19.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr19_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr1.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr1_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr20.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr20_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr21.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr21_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr22.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr22_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr2a.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr2a_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr2b.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr2b_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr3.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr3_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr4.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr4_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr5_h2_hap1.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr5.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr5_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6_cox_hap1.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6_cox_hap1_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6_qbl_hap2.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6_qbl_hap2_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr7.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr7_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr8.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr8_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr9.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr9_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chrM.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chrUn.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chrX.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chrX_random.maf.lzo\n' |
| b |
| diff -r 000000000000 -r cfea1d6354db tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Jul 17 10:56:42 2020 -0400 |
| b |
| @@ -0,0 +1,8 @@ +<!-- Paths are relative to the value of `tool_data_path` in galaxy.ini --> +<tables> + <!-- Locations of MAF files that have been indexed with bx-python --> + <table name="maf_indexes"> + <columns>name, value, indexed_for, exists_in_maf, path</columns> + <file path="maf_indexes.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r cfea1d6354db tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri Jul 17 10:56:42 2020 -0400 |
| b |
| @@ -0,0 +1,8 @@ +<!-- Paths are relative to the value of `tool_data_path` in galaxy.ini --> +<tables> + <!-- Locations of MAF files that have been indexed with bx-python --> + <table name="maf_indexes"> + <columns>name, value, indexed_for, exists_in_maf, path</columns> + <file path="${__HERE__}/test-data/local/maf_indexes.loc" /> + </table> +</tables> |
