Galaxy |

Changeset 0:be7c0c692879 (2024-07-23)

Next changeset 1:ddbace8f3277 (2024-08-27)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv commit 7e7abdef47fdf68f3ca69b75a8477dabc7bfa965

diff -r 000000000000 -r be7c0c692879 gtf_to_position_file.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gtf_to_position_file.py Tue Jul 23 15:43:10 2024 +0000

[

@@ -0,0 +1,146 @@
+#!/usr/bin/env python
+
+
+"""
+Converts GTF files to proprietary formats.
+"""
+
+
+# Import statements
+import argparse
+import csv
+import gzip
+import os
+
+
+__author__ = 'Timothy Tickle, Itay Tirosh, Brian Haas'
+__copyright__ = 'Copyright 2016'
+__credits__ = ["Timothy Tickle"]
+__license__ = 'BSD-3'
+__maintainer__ = 'Timothy Tickle'
+__email__ = 'ttickle@bbroadinstitute.org'
+__status__ = 'Development'
+
+
+def open_file(file_path):
+    """ Open a file, handling gzip if necessary.
+
+    :param file_path: Path to input file
+    :type file_path: String
+
+    :returns: File object
+    """
+    if file_path.endswith('.gz'):
+        return gzip.open(file_path, 'rt')
+    else:
+        return open(file_path, 'r')
+
+
+def convert_to_positional_file(input_gtf, output_positional, attribute_key):
+    """ Convert input GTF file to positional file.
+
+    :param input_gtf: Path to input gtf file
+    :type input_gtf: String
+    :param output_positional: Path to output positional file
+    :type output_positional: String
+    :param attribute_key: Key of the GTF attribute to use for feature/row names
+    :type attribute_key: String
+
+    :returns: Indicator of success (True) or Failure (False)
+    :rtype: boolean
+    """
+
+    if not input_gtf or not os.path.exists(input_gtf):
+        print("".join(["gtf_to_position_file.py:: ",
+                       "Could not find input file : " + input_gtf]))
+        return False
+
+    all_genes_found = set()
+
+    # Holds lines to output after parsing.
+    output_line = []
+    previous_gene = None
+    previous_chr = None
+    gene_positions = []
+
+    # Metrics for the file
+    i_comments = 0
+    i_duplicate_entries = 0
+    i_entries = 0
+    i_accepted_entries = 0
+    i_written_lines = 0
+
+    with open_file(input_gtf) as gtf:
+        gtf_file = csv.reader(gtf, delimiter="\t")
+        for gtf_line in gtf_file:
+            if gtf_line[0][0] == "#":
+                i_comments += 1
+                continue
+            i_entries += 1
+            # Clean up the attribute keys and match the one of interest.
+            attributes = gtf_line[8].split(";")
+            attributes = [entry.strip(" ") for entry in attributes]
+            attributes = [entry.split(" ") for entry in attributes if entry]
+            attributes = [[entry[0].strip('"'), entry[1].strip('"')] for entry in attributes]
+            attributes = dict([[entry[0].split("|")[0], entry[1]] for entry in attributes])
+            if attribute_key in attributes:
+                gene_name = attributes[attribute_key]
+            else:
+                print("Could not find an attribute in the GTF with the name '" + attribute_key + "'. Line=" + "\t".join(gtf_line))
+                exit(99)
+            if not gene_name == previous_gene:
+                if len(gene_positions) > 1 and previous_gene not in all_genes_found:
+                    i_accepted_entries += 1
+                    gene_positions.sort()
+                    output_line.append("\t".join([previous_gene,
+                                                  previous_chr,
+                                                  str(gene_positions[0]),
+                                                  str(gene_positions[-1])]))
+                    all_genes_found.add(previous_gene)
+                gene_positions = []
+            else:
+                i_duplicate_entries += 1
+            gene_positions += [int(gtf_line[3]), int(gtf_line[4])]
+            previous_gene = gene_name
+            previous_chr = gtf_line[0]
+        if previous_gene and previous_chr and len(gene_positions) > 1:
+            i_accepted_entries += 1
+            gene_positions.sort()
+            output_line.append("\t".join([previous_gene,
+                                          previous_chr,
+                                          str(gene_positions[0]),
+                                          str(gene_positions[-1])]))
+
+    with open(output_positional, "w") as positional_file:
+        i_written_lines += len(output_line)
+        positional_file.write("\n".join(output_line))
+
+    # Print metrics
+    print("Number of lines read: " + str(i_entries))
+    print("Number of comments: " + str(i_comments))
+    print("Number of entries: " + str(i_accepted_entries))
+    print("Number of duplicate entries: " + str(i_duplicate_entries))
+    print("Number of entries written: " + str(i_written_lines))
+
+
+if __name__ == "__main__":
+
+    # Parse arguments
+    prsr_arguments = argparse.ArgumentParser(prog='gtf_to_position_file.py',
+                                             description='Convert a GTF file to a positional file.',
+                                             formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    # Add positional argument
+    prsr_arguments.add_argument("input_gtf",
+                                metavar="input_gtf",
+                                help="Path to the input GTF file.")
+    prsr_arguments.add_argument("--attribute_name",
+                                metavar="attribute_name",
+                                default="gene_id",
+                                help="The name of the attribute in the GTF attributes to use instead of gene name, for example 'gene_name' or 'transcript_id'.")
+    prsr_arguments.add_argument("output_positional",
+                                metavar="output_positional",
+                                help="Path for the output positional file.")
+    args = prsr_arguments.parse_args()
+
+    # Run Script
+    convert_to_positional_file(args.input_gtf, args.output_positional, args.attribute_name)

diff -r 000000000000 -r be7c0c692879 infercnv.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/infercnv.xml Tue Jul 23 15:43:10 2024 +0000

[

b'@@ -0,0 +1,608 @@\n+<tool id="infercnv" name="InferCNV" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n+ <description>Infer Copy Number Variation from Single-Cell RNA-Seq Data</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <command detect_errors="exit_code"><![CDATA[\n+ #if $annotation.gene_annotation == "gtf":\n+ ## extract gene order from gtf file\n+ python \'$__tool_directory__/gtf_to_position_file.py\' --attribute_name $attribute \'$gtf_file\' \'gene_order.tabular\' &&\n+ #end if\n+ Rscript \'$infercnv_script\'\n+ ]]></command>\n+ <configfiles>\n+ <configfile name="infercnv_script">\n+ # InferCNV configuration file\n+ # This file is used to specify the parameters for the InferCNV tool\n+ \n+ # load library\n+ library(\'infercnv\')\n+\n+ # create the infercnv object\n+ infercnv_obj = CreateInfercnvObject(\n+ raw_counts_matrix=\'$raw_mtx\', # the matrix of genes (rows) vs. cells (columns) containing the raw counts\n+ #if $annotation.gene_annotation == "gtf":\n+ gene_order_file=\'gene_order.tabular\', # tabular file containing the positions of each gene along each chromosome in the genome.\n+ #end if\n+ #if $annotation.gene_annotation == "local":\n+ gene_order_file=\'$gene_order\', # data file containing the positions of each gene along each chromosome in the genome.\n+ #end if\n+ annotations_file=\'$cell_annotations\', # a description of the cells, indicating the cell type classifications\n+ #if \'$ref_group\':\n+ ref_group_names=c($ref_group), # a vector containing the classifications of the reference (normal) cells to use for infering cnv\n+ #end if\n+ delim="\\t",\n+ #if $max_cell:\n+ max_cells_per_group = $max_cell, #maximun number of cells to use per group. Default=NULL, using all cells defined in the annotations_file. \n+ #end if\n+ #if $max_count:\n+ min_max_counts_per_cell = c($min_count, $max_count), # minimum and maximum counts allowed per cell. Any cells outside this range will be removed from the counts matrix. \n+ #else\n+ min_max_counts_per_cell = c($min_count, +Inf),\n+ #end if\n+ chr_exclude = c($chr_exclude) # chromosomes to exclude from the analysis\n+ )\n+\n+ # perform infercnv operations to reveal cnv signal\n+ infercnv_obj = infercnv::run(\n+ infercnv_obj,\n+ cutoff= $cutoff,\n+ min_cells_per_gene = $min_cells_per_gene,\n+ out_dir="output",\n+ num_ref_groups = NULL, # keep this as default\n+ ref_subtract_use_mean_bounds = TRUE, # keep this as default\n+\n+ ## Smoothing params\n+ window_length = $window_length,\n+ '..b'----------------------\n+MGH36_P1_B02 malignant_MGH36\n+-------------- -------------------------------\n+MGH36_P1_H10 malignant_MGH36\n+============== ===============================\n+\n+\n+The first column is the cell name, and the 2nd column indicates the known cell type.\n+\n+The sample (ie. patient) information is encoded in the attribute name as "malignant_{patient}", which allows the tumor cells to be clustered and plotted according to sample (patient) in the heatmap.\n+\n+\n+.. class:: infomark\n+\n+Only those cells listed in the sample annotations file will be analyzed by inferCNV. This is useful in case you cells of interest are a subset of the total counts matrix, without needing create a new matrix containing the subset of interest.\n+\n+\n+**Gene ordering file**\n+\n+The gene ordering file provides the chromosomal location for each gene. The format is tabular and has **no** column header, simply providing the gene name, chromosome, and gene span:\n+\n+\n+========= ==== ======= =======\n+WASH7P chr1 14363 29806\n+--------- ---- ------- -------\n+LINC00115 chr1 761586 762902\n+--------- ---- ------- -------\n+NOC2L chr1 879584 894689\n+--------- ---- ------- -------\n+MIR200A chr1 1103243 1103332\n+--------- ---- ------- -------\n+SDF4 chr1 1152288 1167411\n+--------- ---- ------- -------\n+UBE2J2 chr1 1189289 1209265\n+========= ==== ======= =======\n+\n+\n+.. class:: infomark\n+\n+Every gene in the counts matrix to be analyzed should have the corresponding gene name and location info provided in this gene ordering file. \n+\n+\n+.. class:: infomark\n+\n+Note, only those genes that exist in both the counts matrix and the gene ordering file will be included in the inferCNV analysis.\n+\n+\n+-----\n+\n+**parameters**\n+\n+.. class:: infomark\n+\n+**Note:** If you do not have reference cells, you can leave *Reference group names* blank, in which case the average signal across all cells will be used to define the baseline. This can work well when there are sufficient differences among the cells included (ie. they do not all show a chromosomal deletion at the same place).\n+\n+.. class:: infomark\n+\n+**Note:** inferCNV expects that you\'ve already filtered out low quality cells. If you need to further impose minimum/maximum read counts per cell, you can include an additional filter in Advanced parameters.\n+\n+.. class:: infomark\n+\n+**Note:** The cutoff value determines which genes will be used for the infercnv analysis. Genes with a mean number of counts across cells will be excluded. For smart-seq (full-length transcript sequencing, typically using cell plate assays rather than droplets), a value of **1** works well. For 10x (and potentially other 3\'-end sequencing and droplet assays, where the count matrix tends to be more sparse), a value of **0.1** is found to generally work well.\n+\n+.. class:: infomark\n+\n+**Note:** The \'cluster_by_groups\' setting indicates to perform separate clustering for the tumor cells according to the patient type, as defined in the cell annotations file.\n+\n+.. class:: infomark\n+\n+**Note:** \n+By default, inferCNV operates at the level of whole samples, such as all cells defined as a certain cell type derived from a single patient. This is the fastest way to run inferCNV, but often not the optimal way, as a given tumor sample may have subpopulations with varied patterns of CNV.\n+By setting "analysis_mode" to "subclusters", inferCNV will attempt to partition cells into groups having consistent patterns of CNV. CNV prediction (via HMM) would then be performed at the level of the subclusters rather than whole samples.\n+\n+\n+.. image:: https://raw.githubusercontent.com/wiki/broadinstitute/infercnv/images/infercnv.logo.png\n+ :height: 500\n+ :width: 600\n+\n+\n+\n+\n+.. _TrinityCTAT: https://github.com/NCIP/Trinity_CTAT/wiki\n+ </help>\n+ <expand macro="citations" />\n+</tool>\n\\ No newline at end of file\n'

diff -r 000000000000 -r be7c0c692879 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue Jul 23 15:43:10 2024 +0000

@@ -0,0 +1,23 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.20.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">24.1</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">bioconductor-infercnv</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">@Manual{github,
+                title = {inferCNV of the Trinity CTAT Project.},
+                author = {Timothy Tickle and Itay Tirosh and Christophe Georgescu and Maxwell Brown and Brian Haas},
+                organization = {Klarman Cell Observatory, Broad Institute of MIT and Harvard},
+                address = {Cambridge, MA, USA},
+                year = {2019},
+                url = {https://github.com/broadinstitute/inferCNV}}
+            </citation>
+        </citations>
+    </xml>
+</macros>

diff -r 000000000000 -r be7c0c692879 test-data/annotations_file.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotations_file.tabular Tue Jul 23 15:43:10 2024 +0000

@@ -0,0 +1,20 @@
+normal_1 normal
+normal_2 normal
+normal_3 normal
+normal_4 normal
+normal_5 normal
+normal_6 normal
+normal_7 normal
+normal_8 normal
+normal_9 normal
+normal_10 normal
+tumor_grp_1_cell_1 tumor
+tumor_grp_1_cell_2 tumor
+tumor_grp_1_cell_3 tumor
+tumor_grp_1_cell_4 tumor
+tumor_grp_1_cell_5 tumor
+tumor_grp_1_cell_6 tumor
+tumor_grp_1_cell_7 tumor
+tumor_grp_1_cell_8 tumor
+tumor_grp_1_cell_9 tumor
+tumor_grp_1_cell_10 tumor

diff -r 000000000000 -r be7c0c692879 test-data/gencode_downsampled.EXAMPLE_ONLY_DONT_REUSE.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gencode_downsampled.EXAMPLE_ONLY_DONT_REUSE.txt Tue Jul 23 15:43:10 2024 +0000

b'@@ -0,0 +1,10338 @@\n+WASH7P\tchr1\t14363\t29806\n+LINC00115\tchr1\t761586\t762902\n+NOC2L\tchr1\t879584\t894689\n+MIR200A\tchr1\t1103243\t1103332\n+SDF4\tchr1\t1152288\t1167411\n+UBE2J2\tchr1\t1189289\t1209265\n+SCNN1D\tchr1\t1215816\t1227409\n+ACAP3\tchr1\t1227756\t1244989\n+PUSL1\tchr1\t1243947\t1247057\n+CPSF3L\tchr1\t1246965\t1260071\n+AURKAIP1\tchr1\t1309110\t1310875\n+CCNL2\tchr1\t1321091\t1334708\n+MRPL20\tchr1\t1337288\t1342693\n+ANKRD65\tchr1\t1353800\t1357149\n+ATAD3B\tchr1\t1407143\t1433228\n+SSU72\tchr1\t1477053\t1510249\n+MMP23B\tchr1\t1567474\t1570639\n+SLC35E2B\tchr1\t1592939\t1624167\n+SLC35E2\tchr1\t1656277\t1677431\n+GNB1\tchr1\t1716729\t1822495\n+GABRD\tchr1\t1950780\t1962192\n+PRKCZ\tchr1\t1981909\t2116834\n+C1orf86\tchr1\t2115903\t2144159\n+RER1\tchr1\t2323267\t2336883\n+PEX10\tchr1\t2336236\t2345236\n+PANK4\tchr1\t2439972\t2458039\n+TNFRSF14\tchr1\t2487078\t2496821\n+FAM213B\tchr1\t2517930\t2522908\n+WRAP73\tchr1\t3547331\t3569325\n+LRRC47\tchr1\t3696784\t3713068\n+DFFB\tchr1\t3773845\t3801993\n+C1orf174\tchr1\t3805689\t3816857\n+MIR4417\tchr1\t5624131\t5624203\n+RPL22\tchr1\t6241329\t6269449\n+ICMT\tchr1\t6281253\t6296032\n+ACOT7\tchr1\t6324329\t6454451\n+NOL9\tchr1\t6581407\t6614595\n+KLHL21\tchr1\t6650784\t6674667\n+PHF13\tchr1\t6673745\t6684093\n+THAP3\tchr1\t6684926\t6695646\n+DNAJC11\tchr1\t6694228\t6761984\n+CAMTA1\tchr1\t6845384\t7829766\n+VAMP3\tchr1\t7831329\t7841492\n+PARK7\tchr1\t8014351\t8045565\n+ERRFI1\tchr1\t8064464\t8086368\n+SLC45A1\tchr1\t8377886\t8404227\n+RERE\tchr1\t8412457\t8877702\n+ENO1\tchr1\t8921061\t8939308\n+SLC2A5\tchr1\t9095166\t9148537\n+SPSB1\tchr1\t9352939\t9429591\n+CLSTN1\tchr1\t9789084\t9884584\n+LZIC\tchr1\t9982173\t10003465\n+NMNAT1\tchr1\t10003486\t10045559\n+UBE4B\tchr1\t10092890\t10241297\n+KIF1B\tchr1\t10270863\t10441661\n+PGD\tchr1\t10458649\t10480201\n+DFFA\tchr1\t10516579\t10532583\n+TARDBP\tchr1\t11072414\t11085796\n+SRM\tchr1\t11114641\t11120081\n+EXOSC10\tchr1\t11126675\t11159938\n+MTOR\tchr1\t11166592\t11322564\n+UBIAD1\tchr1\t11333263\t11356106\n+PTCHD2\tchr1\t11539223\t11597641\n+FBXO44\tchr1\t11714432\t11723384\n+FBXO6\tchr1\t11724181\t11734411\n+MAD2L2\tchr1\t11734537\t11751707\n+AGTRAP\tchr1\t11796141\t11814859\n+CLCN6\tchr1\t11866207\t11903201\n+NPPA\tchr1\t11905766\t11908402\n+RNU5E-1\tchr1\t11968209\t11968328\n+PLOD1\tchr1\t11994262\t12035595\n+MFN2\tchr1\t12040238\t12073571\n+MIIP\tchr1\t12079523\t12092102\n+TNFRSF1B\tchr1\t12227060\t12269285\n+DHRS3\tchr1\t12627939\t12677737\n+PRAMEF10\tchr1\t12952727\t12958101\n+PRAMEF16\tchr1\t13495254\t13498260\n+PDPN\tchr1\t13909960\t13944452\n+PRDM2\tchr1\t14026693\t14151574\n+KAZN\tchr1\t14925200\t15444539\n+CASP9\tchr1\t15817327\t15853029\n+DNAJC16\tchr1\t15853308\t15918874\n+FBLIM1\tchr1\t16083102\t16113089\n+SPEN\tchr1\t16174359\t16266955\n+ZBTB17\tchr1\t16268364\t16302627\n+FBXO42\tchr1\t16573334\t16678949\n+SZRD1\tchr1\t16679070\t16724640\n+NECAP2\tchr1\t16767167\t16786573\n+NBPF1\tchr1\t16888814\t16940057\n+CROCCP2\tchr1\t16944751\t16971178\n+MIR3675\tchr1\t17185444\t17185516\n+SDHB\tchr1\t17345217\t17380665\n+PADI2\tchr1\t17393256\t17445948\n+RCC2\tchr1\t17733256\t17766220\n+ARHGEF10L\tchr1\t17866330\t18024369\n+IGSF21\tchr1\t18434240\t18704977\n+UBR4\tchr1\t19401000\t19536770\n+EMC1\tchr1\t19542158\t19578046\n+MRTO4\tchr1\t19578033\t19586622\n+AKR7A2\tchr1\t19630459\t19638640\n+PQLC2\tchr1\t19638820\t19655794\n+CAPZB\tchr1\t19665267\t19812066\n+MINOS1\tchr1\t19923477\t19956314\n+TMCO4\tchr1\t20008706\t20126438\n+VWA5B1\tchr1\t20617412\t20681387\n+CAMK2N1\tchr1\t20808884\t20812713\n+MUL1\tchr1\t20825943\t20834654\n+DDOST\tchr1\t20978270\t20988000\n+HP1BP3\tchr1\t21069154\t21113816\n+EIF4G3\tchr1\t21132963\t21503377\n+RAP1GAP\tchr1\t21922708\t21995801\n+USP48\tchr1\t22004791\t22110099\n+CELA3A\tchr1\t22328149\t22339032\n+LINC00339\tchr1\t22351681\t22357716\n+CDC42\tchr1\t22379120\t22419437\n+C1QA\tchr1\t22962999\t22966101\n+C1QC\tchr1\t22970123\t22974603\n+C1QB\tchr1\t22979255\t22988031\n+MIR4684\tchr1\t23046010\t23046091\n+HNRNPR\tchr1\t23630264\t23670829\n+ZNF436\tchr1\t23685941\t23695935\n+C1orf213\tchr1\t23695490\t23698332\n+ASAP3\tchr1\t23755056\t23811061\n+ID3\tchr1\t23884409\t23886285\n+RPL11\tchr1\t24018269\t24022915\n+TCEB3\tchr1\t24069645\t24088549\n+PITHD1\tchr1\t24104895\t24114722\n+LYPLA2\tchr1\t24117460\t24122029\n+GALE\tchr1\t24122089\t24127271\n+HMGCL\tchr1\t24128375\t24165110\n+FUCA1\tchr1\t24171567\t24194784\n+PNRC2\tchr1\t24285599\t24289952\n+SRSF10\tchr1\t24291294\t24307417\n+NIPAL3\tchr1\t24742284\t24799'..b'\t118925606\n+UPF3B\tchrX\t118967985\t118986961\n+RNF113A\tchrX\t119004497\t119005791\n+NDUFA1\tchrX\t119005450\t119010625\n+NKAP\tchrX\t119059014\t119077735\n+ZBTB33\tchrX\t119384607\t119392253\n+TMEM255A\tchrX\t119392505\t119445411\n+LAMP2\tchrX\t119561682\t119603220\n+CUL4B\tchrX\t119658464\t119709649\n+MCTS1\tchrX\t119727865\t119754929\n+C1GALT1C1\tchrX\t119759648\t119764005\n+CT47A9\tchrX\t120077421\t120080733\n+GRIA3\tchrX\t122318006\t122624766\n+THOC2\tchrX\t122734412\t122866906\n+XIAP\tchrX\t122993574\t123047829\n+STAG2\tchrX\t123094062\t123556514\n+SMARCA1\tchrX\t128580480\t128657477\n+OCRL\tchrX\t128673826\t128726538\n+SASH3\tchrX\t128913955\t128929177\n+ZDHHC9\tchrX\t128937264\t128977885\n+UTP14A\tchrX\t129040097\t129063737\n+AIFM1\tchrX\t129263337\t129299861\n+RAB33A\tchrX\t129305623\t129318844\n+ZNF280C\tchrX\t129336685\t129402873\n+SLC25A14\tchrX\t129473874\t129507335\n+RBMX2\tchrX\t129535943\t129547317\n+FAM45B\tchrX\t129628939\t129630562\n+MST4\tchrX\t131157293\t131209971\n+RAP2C\tchrX\t131337053\t131353471\n+MIR363\tchrX\t133303408\t133303482\n+PHF6\tchrX\t133507283\t133562820\n+HPRT1\tchrX\t133594183\t133654543\n+MIR450A1\tchrX\t133674371\t133674461\n+FAM122C\tchrX\t133930819\t133988640\n+MOSPD1\tchrX\t134021656\t134049297\n+FAM127C\tchrX\t134154543\t134156559\n+FAM127A\tchrX\t134166333\t134167576\n+FAM127B\tchrX\t134184962\t134186226\n+ZNF75D\tchrX\t134382867\t134478012\n+ZNF449\tchrX\t134478721\t134497077\n+DDX26B\tchrX\t134654584\t134716435\n+CT45A1\tchrX\t134847185\t134857354\n+MMGT1\tchrX\t135044229\t135056222\n+SLC9A6\tchrX\t135067598\t135129423\n+FHL1\tchrX\t135229559\t135293518\n+MAP7D3\tchrX\t135295381\t135338641\n+HTATSF1\tchrX\t135579238\t135594505\n+ARHGEF6\tchrX\t135747706\t135864247\n+RBMX\tchrX\t135930163\t135962923\n+ZIC3\tchrX\t136648301\t136659850\n+SOX3\tchrX\t139585152\t139587225\n+CDR1\tchrX\t139865425\t139866723\n+LDOC1\tchrX\t140269934\t140271310\n+SPANXD\tchrX\t140785568\t140786896\n+SLITRK2\tchrX\t144899350\t144907360\n+MIR506\tchrX\t146312238\t146312361\n+FMR1\tchrX\t146993469\t147032645\n+FMR1NB\tchrX\t147062849\t147108187\n+IDS\tchrX\t148558521\t148615470\n+CXorf40A\tchrX\t148621900\t148632055\n+TMEM185A\tchrX\t148678216\t148713568\n+MAGEA8\tchrX\t149009941\t149014609\n+CXorf40B\tchrX\t149097745\t149107029\n+MTM1\tchrX\t149737069\t149841795\n+MTMR1\tchrX\t149861435\t149933576\n+CD99L2\tchrX\t149934810\t150067289\n+HMGB3\tchrX\t150148982\t150159248\n+VMA21\tchrX\t150564987\t150577836\n+GABRA3\tchrX\t151334706\t151619830\n+CSAG1\tchrX\t151903228\t151909518\n+CETN2\tchrX\t151995517\t151999321\n+NSDHL\tchrX\t151999511\t152038273\n+PNMA6A\tchrX\t152240839\t152340864\n+ZNF275\tchrX\t152599613\t152625568\n+HAUS7\tchrX\t152713124\t152760978\n+FAM58A\tchrX\t152853377\t152865500\n+DUSP9\tchrX\t152907946\t152916781\n+SLC6A8\tchrX\t152953554\t152962048\n+BCAP31\tchrX\t152965947\t152990152\n+PLXNB3\tchrX\t153029651\t153044801\n+IDH3G\tchrX\t153051221\t153059978\n+SSR4\tchrX\t153058971\t153063960\n+L1CAM\tchrX\t153126969\t153174677\n+ARHGAP4\tchrX\t153172821\t153200452\n+NAA10\tchrX\t153194695\t153200676\n+HCFC1\tchrX\t153213004\t153237258\n+TMEM187\tchrX\t153237778\t153248646\n+IRAK1\tchrX\t153275951\t153285431\n+MECP2\tchrX\t153287024\t153363212\n+FLNA\tchrX\t153576892\t153603006\n+EMD\tchrX\t153607557\t153609883\n+RPL10\tchrX\t153618315\t153637504\n+TAZ\tchrX\t153639854\t153650065\n+ATP6AP1\tchrX\t153656978\t153664862\n+GDI1\tchrX\t153665266\t153671814\n+FAM50A\tchrX\t153672473\t153679002\n+LAGE3\tchrX\t153706028\t153707596\n+UBL4A\tchrX\t153712056\t153715009\n+FAM3A\tchrX\t153733350\t153744566\n+G6PD\tchrX\t153759606\t153775787\n+IKBKG\tchrX\t153769414\t153796782\n+DKC1\tchrX\t153991031\t154005964\n+MPP1\tchrX\t154006959\t154049282\n+F8\tchrX\t154064063\t154255215\n+FUNDC2\tchrX\t154254255\t154288578\n+BRCC3\tchrX\t154299695\t154351349\n+VBP1\tchrX\t154425284\t154468098\n+RAB39B\tchrX\t154487526\t154493874\n+CLIC2\tchrX\t154505500\t154563966\n+TMLHE\tchrX\t154719776\t154899605\n+VAMP7\tchrX\t155110956\t155173433\n+RPS4Y1\tchrY\t2709527\t2800041\n+TTTY1B\tchrY\t6258472\t6279605\n+TTTY18\tchrY\t8551411\t8551919\n+RBMY3AP\tchrY\t9448180\t9458885\n+TTTY15\tchrY\t14774265\t14804162\n+USP9Y\tchrY\t14813160\t14972764\n+DDX3Y\tchrY\t15016019\t15032390\n+NLGN4Y\tchrY\t16634518\t16957530\n+CDY2B\tchrY\t19989290\t19992100\n+KDM5D\tchrY\t21865751\t21906825\n+EIF1AY\tchrY\t22737611\t22755040\n+PRY2\tchrY\t24217903\t24242154\n+BPY2\tchrY\t25119966\t25151612\n+BPY2C\tchrY\t27177048\t27208695\n'

diff -r 000000000000 -r be7c0c692879 test-data/gene_order.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_order.tabular Tue Jul 23 15:43:10 2024 +0000

b'@@ -0,0 +1,395 @@\n+WASH7P\tchr1\t14404\t29570\n+LINC00115\tchr1\t826206\t827522\n+NOC2L\tchr1\t944204\t959309\n+MIR200A\tchr1\t1167863\t1167952\n+SDF4\tchr1\t1216908\t1232031\n+UBE2J2\tchr1\t1253909\t1273885\n+SCNN1D\tchr1\t1280436\t1292029\n+ACAP3\tchr1\t1292376\t1309609\n+PUSL1\tchr1\t1308567\t1311677\n+AURKAIP1\tchr1\t1373730\t1375495\n+CCNL2\tchr1\t1385711\t1399328\n+MRPL20\tchr1\t1401908\t1407313\n+ANKRD65\tchr1\t1418420\t1421769\n+ATAD3B\tchr1\t1471769\t1497848\n+SSU72\tchr1\t1541673\t1574869\n+MMP23B\tchr1\t1632095\t1635263\n+SLC35E2B\tchr1\t1659529\t1692728\n+SLC35E2\tchr1\t1724838\t1745992\n+GNB1\tchr1\t1785285\t1891117\n+GABRD\tchr1\t2019298\t2030758\n+PRKCZ\tchr1\t2050470\t2185395\n+RER1\tchr1\t2391775\t2405444\n+PEX10\tchr1\t2403964\t2413797\n+PANK4\tchr1\t2508533\t2526628\n+TNFRSF14\tchr1\t2555639\t2565382\n+FAM213B\tchr1\t2586491\t2591469\n+WRAP73\tchr1\t3630767\t3652761\n+LRRC47\tchr1\t3778558\t3796504\n+DFFB\tchr1\t3857267\t3885429\n+C1orf174\tchr1\t3889125\t3900293\n+MIR4417\tchr1\t5564071\t5564143\n+RPL22\tchr1\t6181269\t6209389\n+ICMT\tchr1\t6221193\t6235972\n+ACOT7\tchr1\t6264269\t6394391\n+NOL9\tchr1\t6521347\t6554535\n+KLHL21\tchr1\t6590724\t6614607\n+PHF13\tchr1\t6613685\t6624033\n+THAP3\tchr1\t6624866\t6635586\n+DNAJC11\tchr1\t6634168\t6701924\n+CAMTA1\tchr1\t6785324\t7769706\n+VAMP3\tchr1\t7771269\t7781432\n+PARK7\tchr1\t7954291\t7985505\n+ERRFI1\tchr1\t8004404\t8026308\n+SLC45A1\tchr1\t8317826\t8344167\n+RERE\tchr1\t8352397\t8817643\n+ENO1\tchr1\t8861002\t8879249\n+SLC2A5\tchr1\t9035107\t9088478\n+SPSB1\tchr1\t9292880\t9369532\n+CLSTN1\tchr1\t9729026\t9824526\n+LZIC\tchr1\t9922113\t9943407\n+NMNAT1\tchr1\t9943428\t9985501\n+UBE4B\tchr1\t10032832\t10181239\n+KIF1B\tchr1\t10210805\t10381603\n+PGD\tchr1\t10398592\t10420144\n+DFFA\tchr1\t10456522\t10472526\n+TARDBP\tchr1\t11012344\t11026420\n+SRM\tchr1\t11054584\t11060024\n+EXOSC10\tchr1\t11066618\t11099881\n+MTOR\tchr1\t11106535\t11262507\n+UBIAD1\tchr1\t11273206\t11296049\n+FBXO44\tchr1\t11654375\t11663327\n+FBXO6\tchr1\t11664124\t11674354\n+MAD2L2\tchr1\t11674480\t11691650\n+AGTRAP\tchr1\t11736084\t11754802\n+CLCN6\tchr1\t11806096\t11843144\n+NPPA\tchr1\t11845709\t11848345\n+RNU5E-1\tchr1\t11908152\t11908271\n+PLOD1\tchr1\t11934205\t11975538\n+MFN2\tchr1\t11980181\t12013514\n+MIIP\tchr1\t12019466\t12032045\n+TNFRSF1B\tchr1\t12167003\t12209228\n+SNORA70\tchr1\t12221148\t12221271\n+DHRS3\tchr1\t12567910\t12617731\n+PRAMEF10\tchr1\t12892896\t12898270\n+PDPN\tchr1\t13583465\t13617957\n+PRDM2\tchr1\t13700198\t13825079\n+KAZN\tchr1\t13892792\t15118043\n+CASP9\tchr1\t15490832\t15526534\n+DNAJC16\tchr1\t15526813\t15592379\n+FBLIM1\tchr1\t15756607\t15786594\n+SPEN\tchr1\t15847864\t15940460\n+ZBTB17\tchr1\t15941869\t15976132\n+FBXO42\tchr1\t16246839\t16352454\n+SZRD1\tchr1\t16352575\t16398145\n+NECAP2\tchr1\t16440672\t16460078\n+NBPF1\tchr1\t16562319\t16613562\n+CROCCP2\tchr1\t16618253\t16657232\n+MIR3675\tchr1\t16858949\t16859021\n+SDHB\tchr1\t17018722\t17054170\n+PADI2\tchr1\t17066761\t17119435\n+RCC2\tchr1\t17406760\t17439724\n+ARHGEF10L\tchr1\t17539835\t17697874\n+IGSF21\tchr1\t18107746\t18378483\n+UBR4\tchr1\t19074506\t19210276\n+EMC1\tchr1\t19215664\t19251552\n+MRTO4\tchr1\t19251539\t19260128\n+AKR7A2\tchr1\t19303965\t19312146\n+PQLC2\tchr1\t19312326\t19329300\n+CAPZB\tchr1\t19338776\t19485539\n+MINOS1\tchr1\t19596977\t19629821\n+TMCO4\tchr1\t19682213\t19799945\n+VWA5B1\tchr1\t20290919\t20354894\n+CAMK2N1\tchr1\t20482391\t20486220\n+MUL1\tchr1\t20499448\t20508161\n+DDOST\tchr1\t20651767\t20661544\n+HP1BP3\tchr1\t20742661\t20787323\n+EIF4G3\tchr1\t20806292\t21176888\n+RAP1GAP\tchr1\t21596215\t21669363\n+USP48\tchr1\t21678298\t21783606\n+CELA3A\tchr1\t22001656\t22012539\n+LINC00339\tchr1\t22024558\t22031223\n+CDC42\tchr1\t22052627\t22092946\n+C1QA\tchr1\t22636506\t22639608\n+C1QC\tchr1\t22643630\t22648110\n+C1QB\tchr1\t22652762\t22661538\n+MIR4684\tchr1\t22719517\t22719598\n+HNRNPR\tchr1\t23303771\t23344336\n+ZNF436\tchr1\t23359448\t23369442\n+ASAP3\tchr1\t23428563\t23484568\n+ID3\tchr1\t23557918\t23559794\n+RPL11\tchr1\t23691779\t23696425\n+PITHD1\tchr1\t23778405\t23788232\n+LYPLA2\tchr1\t23790970\t23795539\n+GALE\tchr1\t23795599\t23800804\n+HMGCL\tchr1\t23801885\t23838620\n+FUCA1\tchr1\t23845077\t23868294\n+PNRC2\tchr1\t23959109\t23963462\n+SRSF10\tchr1\t23964804\t23980927\n+NIPAL3\tchr1\t24415794\t24472976\n+SRRM1\tchr1\t24631716\t24673267\n+CLIC4\tchr1\t24745357\t24844324\n+SYF2\tchr1\t25222679\t25232502\n+TMEM50A\tchr1\t25337917\t25362361\n+RHCE\tchr1\t25362249\t25430192\n+MTFR'..b'ZT2\tchr1\t43389882\t43454247\n+HYI\tchr1\t43451003\t43453989\n+KDM4A\tchr1\t43650158\t43705515\n+IPO13\tchr1\t43946939\t43968022\n+DPH2\tchr1\t43970000\t43973369\n+ATP6V0B\tchr1\t43974487\t43978295\n+SLC6A9\tchr1\t43991500\t44031467\n+DMAP1\tchr1\t44213455\t44220681\n+ERI3\tchr1\t44221070\t44355260\n+RNF220\tchr1\t44405194\t44651724\n+MIR5584\tchr1\t44545493\t44545552\n+TMEM53\tchr1\t44635238\t44674555\n+RPS8\tchr1\t44775251\t44778779\n+SNORD38B\tchr1\t44778390\t44778458\n+PLK3\tchr1\t44800225\t44805990\n+EIF2B3\tchr1\t44850522\t44986722\n+HECTD3\tchr1\t45002540\t45011329\n+UROD\tchr1\t45012147\t45015575\n+HPDL\tchr1\t45326905\t45328533\n+MUTYH\tchr1\t45329163\t45340470\n+TOE1\tchr1\t45339670\t45343975\n+PRDX1\tchr1\t45511036\t45523047\n+AKR1A1\tchr1\t45550543\t45570049\n+NASP\tchr1\t45583846\t45618904\n+GPBP1L1\tchr1\t45627304\t45688113\n+TMEM69\tchr1\t45687214\t45694443\n+IPP\tchr1\t45694324\t45750650\n+PIK3R3\tchr1\t46040140\t46133036\n+POMGNT1\tchr1\t46188682\t46220305\n+LRRC41\tchr1\t46261196\t46303608\n+UQCRH\tchr1\t46303631\t46316776\n+NSUN4\tchr1\t46340177\t46365152\n+FAAH\tchr1\t46394265\t46413848\n+MKNK1\tchr1\t46557408\t46616843\n+ATPAF1\tchr1\t46632737\t46673867\n+EFCAB14\tchr1\t46675159\t46719064\n+PDZK1IP1\tchr1\t47183593\t47191044\n+CMPK1\tchr1\t47333797\t47378839\n+SPATA6\tchr1\t48295372\t48472208\n+BEND5\tchr1\t48727523\t48776969\n+ELAVL4\tchr1\t50048014\t50203786\n+CDKN2C\tchr1\t50960745\t50974633\n+RNF11\tchr1\t51236271\t51273455\n+EPS15\tchr1\t51354263\t51519328\n+OSBPL9\tchr1\t51577179\t51798427\n+TXNDC12\tchr1\t52020131\t52056171\n+KTI12\tchr1\t52032103\t52033816\n+BTF3L4\tchr1\t52056125\t52090716\n+ZFYVE9\tchr1\t52142094\t52346686\n+ORC1\tchr1\t52372829\t52404459\n+PRPF38A\tchr1\t52404564\t52420839\n+ZCCHC11\tchr1\t52408282\t52553487\n+GPX7\tchr1\t52602372\t52609051\n+ZYG11B\tchr1\t52726467\t52827342\n+SCP2\tchr1\t52927229\t53051703\n+MIR5095\tchr1\t52934930\t52935017\n+CPT2\tchr1\t53196429\t53214197\n+C1orf123\tchr1\t53214099\t53220617\n+MAGOH\tchr1\t53226892\t53238610\n+LRP8\tchr1\t53242364\t53328070\n+YIPF1\tchr1\t53851719\t53889834\n+HSPB11\tchr1\t53916574\t53945929\n+LRRC42\tchr1\t53946077\t53968168\n+TMEM59\tchr1\t54026681\t54053504\n+MRPL37\tchr1\t54184041\t54225464\n+TTC4\tchr1\t54715822\t54742657\n+DHCR24\tchr1\t54849633\t54887218\n+TMEM61\tchr1\t54980792\t54992293\n+USP24\tchr1\t55066359\t55215113\n+DAB1\tchr1\t56994778\t58546734\n+OMA1\tchr1\t58415384\t58546802\n+JUN\tchr1\t58780788\t58784327\n+NFIA\tchr1\t60865259\t61462793\n+TM2D1\tchr1\t61681046\t61725423\n+USP1\tchr1\t62436297\t62451804\n+ATG4C\tchr1\t62784135\t62865513\n+FOXD3\tchr1\t63323041\t63325126\n+ALG6\tchr1\t63367590\t63438562\n+ITGB3BP\tchr1\t63440770\t63593721\n+EFCAB7\tchr1\t63523372\t63572693\n+PGM1\tchr1\t63593276\t63660245\n+RAVER2\tchr1\t64745095\t64833232\n+JAK1\tchr1\t64833229\t64966504\n+AK4\tchr1\t65147549\t65232145\n+DNAJC6\tchr1\t65248219\t65415869\n+LEPROT\tchr1\t65420587\t65436007\n+PDE4B\tchr1\t65792514\t66374579\n+MIR3117\tchr1\t66628440\t66628517\n+MIER1\tchr1\t66924895\t66988619\n+SERBP1\tchr1\t67407810\t67430415\n+GADD45A\tchr1\t67685061\t67688338\n+WLS\tchr1\t68098473\t68233120\n+LRRC40\tchr1\t70144805\t70205620\n+SRSF11\tchr1\t70205682\t70253052\n+ANKRD13C\tchr1\t70260588\t70354734\n+HHLA3\tchr1\t70354805\t70385339\n+CTH\tchr1\t70411218\t70439851\n+ZRANB2\tchr1\t71063291\t71081297\n+NEGR1\tchr1\t71395940\t72282734\n+CRYZ\tchr1\t74705482\t74733408\n+TYW3\tchr1\t74733152\t74766678\n+SLC44A5\tchr1\t75202131\t75611116\n+ACADM\tchr1\t75724347\t75787575\n+RABGGTB\tchr1\t75786197\t75795079\n+ST6GALNAC3\tchr1\t76074719\t76634601\n+PIGK\tchr1\t77088990\t77219430\n+AK5\tchr1\t77282051\t77559969\n+ZZZ3\tchr1\t77562416\t77683419\n+USP33\tchr1\t77695987\t77759852\n+FUBP1\tchr1\t77944055\t77979110\n+DNAJB4\tchr1\t77979175\t78017964\n+IFI44L\tchr1\t78619922\t78646145\n+IFI44\tchr1\t78649796\t78664078\n+TTLL7\tchr1\t83865028\t83999150\n+PRKACB\tchr1\t84078062\t84238498\n+RPF1\tchr1\t84479259\t84497790\n+GNG5\tchr1\t84498325\t84506565\n+C1orf52\tchr1\t85249953\t85259672\n+BCL10\tchr1\t85266248\t85277090\n+DDAH1\tchr1\t85318481\t85578363\n+ZNHIT6\tchr1\t85649423\t85708433\n+ODF2L\tchr1\t86346824\t86396342\n+CLCA4\tchr1\t86547078\t86580754\n+SH3GLB1\tchr1\t86704570\t86748184\n+PKN2\tchr1\t88684222\t88836255\n+GTF2B\tchr1\t88852932\t88891944\n+RBMXL1\tchr1\t88979456\t88992960\n+GBP3\tchr1\t89006666\t89022894\n+LRRC8D\tchr1\t89821014\t89936611\n+ZNF326\tchr1\t89995112\t90035531\n+ZNF644\tchr1\t90915298\t91022272\n\\ No newline at end of file\n'

diff -r 000000000000 -r be7c0c692879 test-data/gene_order_file.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_order_file.tabular Tue Jul 23 15:43:10 2024 +0000

diff -r 000000000000 -r be7c0c692879 test-data/oligodendroglioma_annotations_downsampled.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/oligodendroglioma_annotations_downsampled.txt Tue Jul 23 15:43:10 2024 +0000

@@ -0,0 +1,184 @@
+MGH54_P2_C12 Microglia/Macrophage
+MGH36_P6_F03 Microglia/Macrophage
+MGH53_P4_H08 Microglia/Macrophage
+MGH53_P2_E09 Microglia/Macrophage
+MGH36_P5_E12 Microglia/Macrophage
+MGH54_P2_H07 Microglia/Macrophage
+MGH36_P4_H06 Microglia/Macrophage
+MGH53_P1_C01 Microglia/Macrophage
+MGH36_P4_A10 Microglia/Macrophage
+MGH36_P3_D10 Microglia/Macrophage
+MGH54_P2_F09 Microglia/Macrophage
+MGH36_P7_H06 Microglia/Macrophage
+MGH54_P2_H03 Microglia/Macrophage
+MGH36_P8_A02 Microglia/Macrophage
+MGH53_P2_C08 Microglia/Macrophage
+MGH53_P2_A07 Microglia/Macrophage
+MGH53_P1_F10 Microglia/Macrophage
+MGH36_P3_H06 Microglia/Macrophage
+MGH54_P2_F03 Microglia/Macrophage
+MGH54_P16_F12 Oligodendrocytes (non-malignant)
+MGH54_P12_C10 Oligodendrocytes (non-malignant)
+MGH54_P11_C11 Oligodendrocytes (non-malignant)
+MGH54_P15_D06 Oligodendrocytes (non-malignant)
+MGH54_P16_A03 Oligodendrocytes (non-malignant)
+MGH53_P7_B09 Oligodendrocytes (non-malignant)
+MGH54_P10_G04 Oligodendrocytes (non-malignant)
+MGH53_P2_A02 Oligodendrocytes (non-malignant)
+MGH53_P7_F07 Oligodendrocytes (non-malignant)
+MGH53_P5_G02 Oligodendrocytes (non-malignant)
+MGH53_P11_H03 Oligodendrocytes (non-malignant)
+MGH53_P1_A10 Oligodendrocytes (non-malignant)
+MGH53_P5_H09 Oligodendrocytes (non-malignant)
+MGH53_P11_E03 Oligodendrocytes (non-malignant)
+MGH53_P10_F11 Oligodendrocytes (non-malignant)
+MGH53_P1_D07 Oligodendrocytes (non-malignant)
+MGH53_P2_G04 Oligodendrocytes (non-malignant)
+MGH53_P2_G09 Oligodendrocytes (non-malignant)
+MGH53_P5_F04 Oligodendrocytes (non-malignant)
+MGH53_P11_F08 Oligodendrocytes (non-malignant)
+MGH53_P8_F03 Oligodendrocytes (non-malignant)
+MGH53_P6_B11 Oligodendrocytes (non-malignant)
+MGH53_P6_H06 Oligodendrocytes (non-malignant)
+MGH36_P1_B02 malignant_MGH36
+MGH36_P1_H10 malignant_MGH36
+MGH36_P3_A09 malignant_MGH36
+MGH36_P3_B02 malignant_MGH36
+MGH36_P3_C04 malignant_MGH36
+MGH36_P3_E06 malignant_MGH36
+MGH36_P4_B09 malignant_MGH36
+MGH36_P4_D11 malignant_MGH36
+MGH36_P4_G03 malignant_MGH36
+MGH36_P6_C04 malignant_MGH36
+MGH36_P6_G08 malignant_MGH36
+MGH36_P7_B04 malignant_MGH36
+MGH36_P7_D03 malignant_MGH36
+MGH36_P7_F04 malignant_MGH36
+MGH36_P7_G04 malignant_MGH36
+MGH36_P5_B08 malignant_MGH36
+MGH36_P5_F05 malignant_MGH36
+MGH36_P5_F11 malignant_MGH36
+MGH36_P5_H05 malignant_MGH36
+MGH36_P10_B08 malignant_MGH36
+MGH36_P10_C10 malignant_MGH36
+MGH36_P10_E07 malignant_MGH36
+MGH36_P10_F09 malignant_MGH36
+MGH36_P8_E05 malignant_MGH36
+MGH36_P8_H09 malignant_MGH36
+MGH36_P9_B01 malignant_MGH36
+MGH36_P9_B11 malignant_MGH36
+MGH36_P9_H03 malignant_MGH36
+MGH36_P2_A08 malignant_MGH36
+MGH36_P2_C02 malignant_MGH36
+MGH36_P2_G01 malignant_MGH36
+MGH36_P2_G02 malignant_MGH36
+MGH36_P2_H06 malignant_MGH36
+MGH53_P5_A08 malignant_MGH53
+MGH53_P5_D02 malignant_MGH53
+MGH53_P6_F03 malignant_MGH53
+MGH53_P6_H04 malignant_MGH53
+MGH53_P7_B10 malignant_MGH53
+MGH53_P7_C03 malignant_MGH53
+MGH53_P7_E02 malignant_MGH53
+MGH53_P7_G11 malignant_MGH53
+MGH53_P7_H03 malignant_MGH53
+MGH53_P8_A07 malignant_MGH53
+MGH53_P8_C11 malignant_MGH53
+MGH53_P8_E05 malignant_MGH53
+MGH53_P8_E10 malignant_MGH53
+MGH53_P8_H04 malignant_MGH53
+MGH53_P1_B04 malignant_MGH53
+MGH53_P12_A01 malignant_MGH53
+MGH53_P12_B09 malignant_MGH53
+MGH53_P12_C02 malignant_MGH53
+MGH53_P12_C09 malignant_MGH53
+MGH53_P12_D12 malignant_MGH53
+MGH53_P12_E03 malignant_MGH53
+MGH53_P10_B02 malignant_MGH53
+MGH53_P10_C09 malignant_MGH53
+MGH53_P10_E09 malignant_MGH53
+MGH53_P10_H08 malignant_MGH53
+MGH53_P11_A03 malignant_MGH53
+MGH53_P11_B02 malignant_MGH53
+MGH53_P11_B11 malignant_MGH53
+MGH53_P11_F12 malignant_MGH53
+MGH53_P11_H12 malignant_MGH53
+MGH53_P9_A09 malignant_MGH53
+MGH53_P9_C12 malignant_MGH53
+MGH53_P4_C03 malignant_MGH53
+MGH53_P4_F01 malignant_MGH53
+97_P3_G07 malignant_97
+97_P3_E04 malignant_97
+97_P3_D10 malignant_97
+97_P3_E01 malignant_97
+97_P3_E03 malignant_97
+97_P3_B10 malignant_97
+97_P3_B04 malignant_97
+97_P3_B01 malignant_97
+97_P3_B03 malignant_97
+97_P3_D01 malignant_97
+97_P3_D04 malignant_97
+97_P3_D12 malignant_97
+97_P3_F12 malignant_97
+97_P3_E12 malignant_97
+97_P5_D09 malignant_97
+97_P6_H01 malignant_97
+97_P5_C10 malignant_97
+97_P6_E07 malignant_97
+97_P5_D02 malignant_97
+97_P6_G10 malignant_97
+97_P5_G05 malignant_97
+97_P6_B09 malignant_97
+97_P5_H08 malignant_97
+97_P5_F04 malignant_97
+97_P5_D01 malignant_97
+97_P6_F05 malignant_97
+97_P6_A06 malignant_97
+97_P5_A07 malignant_97
+97_P6_E01 malignant_97
+97_P6_D09 malignant_97
+97_P5_G06 malignant_97
+97_P5_E12 malignant_97
+97_P6_A07 malignant_97
+97_P6_G12 malignant_97
+97_P6_H06 malignant_97
+93_P3_B02 malignant_93
+93_P3_G05 malignant_93
+93_P3_H04 malignant_93
+93_P3_A10 malignant_93
+93_P3_C04 malignant_93
+93_P3_D07 malignant_93
+93_P3_G07 malignant_93
+93_P3_E09 malignant_93
+93_P3_G11 malignant_93
+93_P3_A11 malignant_93
+93_P6_H11 malignant_93
+93_P5_H06 malignant_93
+93_P5_C12 malignant_93
+93_P6_A02 malignant_93
+93_P5_D07 malignant_93
+93_P6_C07 malignant_93
+93_P9_C04 malignant_93
+93_P9_E04 malignant_93
+93_P9_H01 malignant_93
+93_P8_B06 malignant_93
+93_P10_E05 malignant_93
+93_P9_B10 malignant_93
+93_P8_G11 malignant_93
+93_P9_F02 malignant_93
+93_P10_F03 malignant_93
+93_P9_G11 malignant_93
+93_P8_E09 malignant_93
+93_P8_C11 malignant_93
+93_P9_A03 malignant_93
+93_P10_G11 malignant_93
+93_P9_B11 malignant_93
+93_P9_D06 malignant_93
+93_P8_B02 malignant_93
+93_P8_C09 malignant_93
+93_P9_H03 malignant_93
+93_P10_D04 malignant_93
+93_P8_G09 malignant_93
+93_P10_B10 malignant_93
+93_P9_C07 malignant_93
+93_P8_A12 malignant_93

diff -r 000000000000 -r be7c0c692879 test-data/oligodendroglioma_expression_downsampled.counts.matrix.gz

Binary file test-data/oligodendroglioma_expression_downsampled.counts.matrix.gz has changed

diff -r 000000000000 -r be7c0c692879 test-data/output/test1_infercnv.heatmap_thresholds.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output/test1_infercnv.heatmap_thresholds.txt Tue Jul 23 15:43:10 2024 +0000

@@ -0,0 +1,16 @@
+0.510778825104826
+0.576008315090849
+0.641237805076872
+0.706467295062896
+0.771696785048919
+0.836926275034942
+0.902155765020965
+0.967385255006988
+1.03261474499301
+1.09784423497903
+1.16307372496506
+1.22830321495108
+1.2935327049371
+1.35876219492313
+1.42399168490915
+1.48922117489517

diff -r 000000000000 -r be7c0c692879 test-data/output/test1_infercnv.observation_groupings.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output/test1_infercnv.observation_groupings.txt Tue Jul 23 15:43:10 2024 +0000

@@ -0,0 +1,11 @@
+"Dendrogram Group" "Dendrogram Color" "Annotation Group" "Annotation Color"
+"tumor_grp_1_cell_10" "tumor" "#8DD3C7" "1" "#8DD3C7"
+"tumor_grp_1_cell_1" "tumor" "#8DD3C7" "1" "#8DD3C7"
+"tumor_grp_1_cell_5" "tumor" "#8DD3C7" "1" "#8DD3C7"
+"tumor_grp_1_cell_6" "tumor" "#8DD3C7" "1" "#8DD3C7"
+"tumor_grp_1_cell_7" "tumor" "#8DD3C7" "1" "#8DD3C7"
+"tumor_grp_1_cell_3" "tumor" "#8DD3C7" "1" "#8DD3C7"
+"tumor_grp_1_cell_4" "tumor" "#8DD3C7" "1" "#8DD3C7"
+"tumor_grp_1_cell_9" "tumor" "#8DD3C7" "1" "#8DD3C7"
+"tumor_grp_1_cell_8" "tumor" "#8DD3C7" "1" "#8DD3C7"
+"tumor_grp_1_cell_2" "tumor" "#8DD3C7" "1" "#8DD3C7"

diff -r 000000000000 -r be7c0c692879 test-data/output/test1_infercnv.png

Binary file test-data/output/test1_infercnv.png has changed

diff -r 000000000000 -r be7c0c692879 test-data/output/test1_infercnv_subclusters.heatmap_thresholds.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output/test1_infercnv_subclusters.heatmap_thresholds.txt Tue Jul 23 15:43:10 2024 +0000

@@ -0,0 +1,16 @@
+0.539401407315098
+0.60272272515377
+0.666044042992442
+0.729365360831113
+0.792686678669785
+0.856007996508457
+0.919329314347129
+0.9826506321858
+1.04597195002447
+1.10929326786314
+1.17261458570182
+1.23593590354049
+1.29925722137916
+1.36257853921783
+1.4258998570565
+1.48922117489517

diff -r 000000000000 -r be7c0c692879 test-data/output/test1_infercnv_subclusters.observation_groupings.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output/test1_infercnv_subclusters.observation_groupings.txt Tue Jul 23 15:43:10 2024 +0000

@@ -0,0 +1,11 @@
+"Dendrogram Group" "Dendrogram Color" "Annotation Group" "Annotation Color"
+"tumor_grp_1_cell_10" "1" "#8DD3C7" "1" "#8DD3C7"
+"tumor_grp_1_cell_1" "1" "#8DD3C7" "1" "#8DD3C7"
+"tumor_grp_1_cell_9" "1" "#8DD3C7" "1" "#8DD3C7"
+"tumor_grp_1_cell_8" "1" "#8DD3C7" "1" "#8DD3C7"
+"tumor_grp_1_cell_2" "1" "#8DD3C7" "1" "#8DD3C7"
+"tumor_grp_1_cell_4" "1" "#8DD3C7" "1" "#8DD3C7"
+"tumor_grp_1_cell_7" "1" "#8DD3C7" "1" "#8DD3C7"
+"tumor_grp_1_cell_5" "1" "#8DD3C7" "1" "#8DD3C7"
+"tumor_grp_1_cell_3" "1" "#8DD3C7" "1" "#8DD3C7"
+"tumor_grp_1_cell_6" "1" "#8DD3C7" "1" "#8DD3C7"

diff -r 000000000000 -r be7c0c692879 test-data/output/test1_infercnv_subclusters.png

Binary file test-data/output/test1_infercnv_subclusters.png has changed

diff -r 000000000000 -r be7c0c692879 test-data/output/test2_infercnv.heatmap_thresholds.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output/test2_infercnv.heatmap_thresholds.txt Tue Jul 23 15:43:10 2024 +0000

@@ -0,0 +1,16 @@
+0.63966404735049
+0.687708841037092
+0.735753634723693
+0.783798428410294
+0.831843222096896
+0.879888015783497
+0.927932809470098
+0.975977603156699
+1.0240223968433
+1.0720671905299
+1.1201119842165
+1.1681567779031
+1.21620157158971
+1.26424636527631
+1.31229115896291
+1.36033595264951

diff -r 000000000000 -r be7c0c692879 test-data/output/test2_infercnv.observation_groupings.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output/test2_infercnv.observation_groupings.txt Tue Jul 23 15:43:10 2024 +0000

b'@@ -0,0 +1,143 @@\n+"Dendrogram Group" "Dendrogram Color" "Annotation Group" "Annotation Color"\n+"93_P8_G09" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P9_D06" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P8_B02" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P9_C04" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P5_D07" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P3_C04" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P9_A03" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P9_C07" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P10_D04" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P10_F03" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P3_G11" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P3_G05" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P8_C11" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P8_B06" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P3_E09" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P10_B10" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P3_A11" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P9_H01" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P5_C12" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P5_H06" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P9_B11" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P9_E04" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P9_G11" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P3_H04" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P9_H03" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P9_B10" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P8_E09" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P8_A12" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P9_F02" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P3_G07" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P6_C07" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P3_D07" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P10_E05" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P8_G11" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P8_C09" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P3_A10" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P6_H11" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P10_G11" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P6_A02" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"93_P3_B02" "malignant_93_s1" "#8DD3C7" "1" "#8DD3C7"\n+"97_P3_D04" "malignant_97_s1" "#A9A0B2" "2" "#A9A0B2"\n+"97_P3_B03" "malignant_97_s1" "#A9A0B2" "2" "#A9A0B2"\n+"97_P5_D02" "malignant_97_s1" "#A9A0B2" "2" "#A9A0B2"\n+"97_P3_F12" "malignant_97_s1" "#A9A0B2" "2" "#A9A0B2"\n+"97_P6_D09" "malignant_97_s1" "#A9A0B2" "2" "#A9A0B2"\n+"97_P6_B09" "malignant_97_s1" "#A9A0B2" "2" "#A9A0B2"\n+"97_P5_D01" "malignant_97_s1" "#A9A0B2" "2" "#A9A0B2"\n+"97_P5_F04" "malignant_97_s1" "#A9A0B2" "2" "#A9A0B2"\n+"97_P6_G12" "malignant_97_s1" "#A9A0B2" "2" "#A9A0B2"\n+"97_P3_D01" "malignant_97_s1" "#A9A0B2" "2" "#A9A0B2"\n+"97_P6_A06" "malignant_97_s1" "#A9A0B2" "2" "#A9A0B2"\n+"97_P6_F05" "malignant_97_s1" "#A9A0B2" "2" "#A9A0B2"\n+"97_P5_H08" "malignant_97_s1" "#A9A0B2" "2" "#A9A0B2"\n+"97_P6_E01" "malignant_97_s1" "#A9A0B2" "2" "#A9A0B2"\n+"97_P5_A07" "malignant_97_s1" "#A9A0B2" "2" "#A9A0B2"\n+"97_P6_E07" "malignant_97_s1" "#A9A0B2" "2" "#A9A0B2"\n+"97_P5_G06" "malignant_97_s1" "#A9A0B2" "2" "#A9A0B2"\n+"97_P5_D09" "malignant_97_s1" "#A9A0B2" "2" "#A9A0B2"\n+"97_P5_C10" "malignant_97_s1" "#A9A0B2" "2" "#A9A0B2"\n+"97_P6_H01" "malignant_97_s1" "#A9A0B2" "2" "#A9A0B2"\n+"97_P3_E01" "malignant_97_s1" "#A9A0B2" "2" "#A9A0B2"\n+"97_P3_B04" "malignant_97_s1" "#A9A0B2" "2" "#A9A0B2"\n+"97_P3_E12" "malignant_97_s1" "#A9A0B2" "2" "#A9A0B2"\n+"97_P3_B01" "malignant_97_s1" "#A9A0B2" "2" "#A9A0B2"\n+"97_P3_E04" "malignant_97_s1" "#A9A0B2" "2" "#A9A0B2"\n+"97_P6_A07" "malignant_97_s1" "#A9A0B2" "2" "#A9A0B2"\n+"97_P3_D10" "malignant_97_s1" "#A9A0B2" "2" "#A9A0B2"\n+"97_P3_E03" "malignant_97_s1" "#A9A0B2" "2" "#A9A0B2"\n+"97_P3_D12" "malignant_97_s1" "#A9A0B2" "2" "#A9A0B2"\n+"97_P3_B10" "malignant_97_s1" "#A9A0B2" "2" "#A9A0B2"\n+"97_P3_G07" "malignant_97_s1" "#A9A0B2" "2" "#A9'..b' "3" "#F0D1E1"\n+"MGH36_P3_E06" "malignant_MGH36_s1" "#F0D1E1" "3" "#F0D1E1"\n+"MGH36_P10_F09" "malignant_MGH36_s1" "#F0D1E1" "3" "#F0D1E1"\n+"MGH36_P2_G01" "malignant_MGH36_s1" "#F0D1E1" "3" "#F0D1E1"\n+"MGH36_P2_H06" "malignant_MGH36_s1" "#F0D1E1" "3" "#F0D1E1"\n+"MGH36_P1_B02" "malignant_MGH36_s1" "#F0D1E1" "3" "#F0D1E1"\n+"MGH36_P2_C02" "malignant_MGH36_s1" "#F0D1E1" "3" "#F0D1E1"\n+"MGH36_P7_F04" "malignant_MGH36_s1" "#F0D1E1" "3" "#F0D1E1"\n+"MGH36_P3_C04" "malignant_MGH36_s1" "#F0D1E1" "3" "#F0D1E1"\n+"MGH36_P10_C10" "malignant_MGH36_s1" "#F0D1E1" "3" "#F0D1E1"\n+"MGH36_P7_G04" "malignant_MGH36_s1" "#F0D1E1" "3" "#F0D1E1"\n+"MGH36_P5_F05" "malignant_MGH36_s1" "#F0D1E1" "3" "#F0D1E1"\n+"MGH36_P4_G03" "malignant_MGH36_s1" "#F0D1E1" "3" "#F0D1E1"\n+"MGH36_P2_G02" "malignant_MGH36_s1" "#F0D1E1" "3" "#F0D1E1"\n+"MGH36_P5_B08" "malignant_MGH36_s1" "#F0D1E1" "3" "#F0D1E1"\n+"MGH36_P8_E05" "malignant_MGH36_s1" "#F0D1E1" "3" "#F0D1E1"\n+"MGH36_P9_H03" "malignant_MGH36_s1" "#F0D1E1" "3" "#F0D1E1"\n+"MGH36_P6_C04" "malignant_MGH36_s1" "#F0D1E1" "3" "#F0D1E1"\n+"MGH36_P1_H10" "malignant_MGH36_s1" "#F0D1E1" "3" "#F0D1E1"\n+"MGH36_P2_A08" "malignant_MGH36_s1" "#F0D1E1" "3" "#F0D1E1"\n+"MGH36_P10_E07" "malignant_MGH36_s1" "#F0D1E1" "3" "#F0D1E1"\n+"MGH36_P10_B08" "malignant_MGH36_s1" "#F0D1E1" "3" "#F0D1E1"\n+"MGH36_P3_B02" "malignant_MGH36_s1" "#F0D1E1" "3" "#F0D1E1"\n+"MGH36_P9_B11" "malignant_MGH36_s1" "#F0D1E1" "3" "#F0D1E1"\n+"MGH36_P7_B04" "malignant_MGH36_s1" "#F0D1E1" "3" "#F0D1E1"\n+"MGH36_P7_D03" "malignant_MGH36_s1" "#F0D1E1" "3" "#F0D1E1"\n+"MGH36_P4_D11" "malignant_MGH36_s1" "#F0D1E1" "3" "#F0D1E1"\n+"MGH36_P6_G08" "malignant_MGH36_s1" "#F0D1E1" "3" "#F0D1E1"\n+"MGH36_P5_F11" "malignant_MGH36_s1" "#F0D1E1" "3" "#F0D1E1"\n+"MGH36_P4_B09" "malignant_MGH36_s1" "#F0D1E1" "3" "#F0D1E1"\n+"MGH36_P8_H09" "malignant_MGH36_s1" "#F0D1E1" "3" "#F0D1E1"\n+"MGH36_P3_A09" "malignant_MGH36_s1" "#F0D1E1" "3" "#F0D1E1"\n+"MGH53_P4_F01" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P10_E09" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P7_G11" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P8_A07" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P12_E03" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P10_H08" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P8_H04" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P5_A08" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P7_C03" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P9_A09" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P6_H04" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P8_E10" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P11_A03" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P11_B11" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P11_H12" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P12_B09" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P12_C02" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P7_B10" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P11_B02" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P12_C09" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P10_B02" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P9_C12" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P7_H03" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P7_E02" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P4_C03" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P12_D12" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P1_B04" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P11_F12" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P12_A01" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P10_C09" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P5_D02" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P8_E05" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P8_C11" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n+"MGH53_P6_F03" "malignant_MGH53_s1" "#FFED6F" "4" "#FFED6F"\n'

diff -r 000000000000 -r be7c0c692879 test-data/output/test2_infercnv.png

Binary file test-data/output/test2_infercnv.png has changed

diff -r 000000000000 -r be7c0c692879 test-data/output/test2_infercnv_subclusters.heatmap_thresholds.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output/test2_infercnv_subclusters.heatmap_thresholds.txt Tue Jul 23 15:43:10 2024 +0000

@@ -0,0 +1,16 @@
+0.640334495133733
+0.688334592301451
+0.73633468946917
+0.784334786636888
+0.832334883804607
+0.880334980972325
+0.928335078140044
+0.976335175307762
+1.02433527247548
+1.0723353696432
+1.12033546681092
+1.16833556397864
+1.21633566114635
+1.26433575831407
+1.31233585548179
+1.36033595264951

diff -r 000000000000 -r be7c0c692879 test-data/output/test2_infercnv_subclusters.observation_groupings.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output/test2_infercnv_subclusters.observation_groupings.txt Tue Jul 23 15:43:10 2024 +0000

@@ -0,0 +1,143 @@
+"Dendrogram Group" "Dendrogram Color" "Annotation Group" "Annotation Color"
+"93_P8_B02" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P10_G11" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P9_H01" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P8_C09" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P3_B02" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P5_C12" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P9_B11" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P9_G11" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P5_H06" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P6_C07" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P9_E04" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P6_H11" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P3_A10" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P9_C04" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P3_D07" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P3_C04" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P10_D04" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P6_A02" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P8_A12" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P3_G07" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P9_F02" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P10_E05" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P8_G11" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P9_H03" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P8_C11" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P3_G11" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P3_G05" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P8_B06" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P3_E09" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P5_D07" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P10_B10" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P3_A11" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P9_B10" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P3_H04" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P8_E09" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P9_D06" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P9_A03" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P8_G09" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P9_C07" "1" "#8DD3C7" "1" "#8DD3C7"
+"93_P10_F03" "1" "#8DD3C7" "1" "#8DD3C7"
+"97_P6_H06" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P6_G10" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P5_G05" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P3_D10" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P3_E03" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P6_F05" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P3_D12" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P3_B01" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P3_G07" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P5_E12" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P6_D09" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P3_F12" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P5_G06" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P6_B09" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P6_E01" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P5_H08" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P6_E07" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P5_A07" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P5_D09" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P5_D01" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P5_F04" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P6_G12" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P5_C10" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P3_D04" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P3_B03" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P5_D02" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P6_H01" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P3_E01" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P6_A06" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P3_B10" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P3_E04" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P6_A07" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P3_D01" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P3_E12" "1" "#8DD3C7" "2" "#A9A0B2"
+"97_P3_B04" "1" "#8DD3C7" "2" "#A9A0B2"
+"MGH36_P9_B01" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P3_E06" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P5_H05" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P10_F09" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P2_H06" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P2_G01" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P1_B02" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P2_C02" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P10_B08" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P2_A08" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P7_B04" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P4_D11" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P1_H10" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P3_A09" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P7_D03" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P6_G08" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P9_H03" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P6_C04" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P7_G04" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P5_F05" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P5_B08" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P8_E05" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P10_C10" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P10_E07" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P4_G03" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P2_G02" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P7_F04" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P3_C04" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P4_B09" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P8_H09" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P5_F11" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P3_B02" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH36_P9_B11" "1" "#8DD3C7" "3" "#F0D1E1"
+"MGH53_P10_B02" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P7_G11" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P12_E03" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P10_E09" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P6_F03" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P10_H08" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P12_C09" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P11_B11" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P11_H12" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P10_C09" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P8_E05" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P8_C11" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P8_H04" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P12_A01" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P8_A07" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P5_A08" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P7_C03" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P11_B02" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P12_B09" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P7_B10" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P12_C02" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P11_F12" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P7_H03" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P7_E02" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P4_C03" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P12_D12" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P1_B04" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P9_C12" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P4_F01" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P9_A09" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P8_E10" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P11_A03" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P6_H04" "1" "#8DD3C7" "4" "#FFED6F"
+"MGH53_P5_D02" "1" "#8DD3C7" "4" "#FFED6F"

diff -r 000000000000 -r be7c0c692879 test-data/output/test2_infercnv_subclusters.png

Binary file test-data/output/test2_infercnv_subclusters.png has changed

diff -r 000000000000 -r be7c0c692879 test-data/output/test3_infercnv.median_filtered.png

Binary file test-data/output/test3_infercnv.median_filtered.png has changed

diff -r 000000000000 -r be7c0c692879 test-data/output/test4_infercnv.heatmap_thresholds.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output/test4_infercnv.heatmap_thresholds.txt Tue Jul 23 15:43:10 2024 +0000

@@ -0,0 +1,16 @@
+0.718141125334214
+0.755722308622985
+0.793303491911757
+0.830884675200528
+0.8684658584893
+0.906047041778071
+0.943628225066843
+0.981209408355614
+1.01879059164439
+1.05637177493316
+1.09395295822193
+1.1315341415107
+1.16911532479947
+1.20669650808824
+1.24427769137701
+1.28185887466579

diff -r 000000000000 -r be7c0c692879 test-data/raw_counts_matrix.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/raw_counts_matrix.tabular Tue Jul 23 15:43:10 2024 +0000

b'@@ -0,0 +1,8253 @@\n+normal_9\ttumor_grp_1_cell_8\ttumor_grp_1_cell_3\tnormal_7\tnormal_5\tnormal_10\tnormal_4\tnormal_2\ttumor_grp_1_cell_10\tnormal_8\tnormal_3\ttumor_grp_1_cell_6\ttumor_grp_1_cell_4\ttumor_grp_1_cell_7\tnormal_1\ttumor_grp_1_cell_5\ttumor_grp_1_cell_1\ttumor_grp_1_cell_9\tnormal_6\ttumor_grp_1_cell_2\n+KIF1B\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t11\t0\t1\t0\t13\t0\t0\t0\t0\n+PGD\t0\t366\t62\t125\t121\t0\t13\t0\t132\t68\t0\t193\t0\t0\t0\t0\t4\t0\t93\t162\n+DFFA\t0\t0\t0\t0\t0\t0\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\n+CASZ1\t0\t2\t0\t0\t0\t0\t0\t0\t4\t0\t9\t0\t0\t0\t0\t0\t0\t0\t3\t0\n+TARDBP\t0\t0\t38\t36\t0\t0\t0\t0\t16\t23\t0\t0\t54\t0\t0\t0\t0\t0\t0\t0\n+SRM\t12\t4\t0\t0\t9\t0\t10\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\n+EXOSC10\t0\t18\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t15\t0\t0\t14\t0\n+MTOR\t0\t98\t35\t0\t36\t0\t0\t14\t0\t0\t0\t90\t0\t0\t101\t57\t72\t0\t0\t0\n+UBIAD1\t0\t0\t7\t18\t166\t74\t0\t28\t0\t0\t0\t0\t0\t0\t93\t81\t9\t24\t0\t0\n+FBXO44\t26\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FBXO6\t18\t0\t6\t0\t0\t0\t0\t11\t0\t0\t2\t0\t14\t0\t14\t0\t0\t0\t0\t0\n+MAD2L2\t0\t0\t0\t0\t0\t11\t0\t1\t0\t0\t0\t0\t13\t0\t0\t0\t18\t0\t12\t0\n+AGTRAP\t36\t15\t1\t0\t0\t29\t26\t19\t0\t37\t56\t0\t46\t0\t0\t0\t0\t39\t12\t0\n+MTHFR\t31\t91\t126\t0\t0\t0\t0\t0\t50\t0\t0\t0\t139\t100\t56\t25\t0\t85\t55\t58\n+CLCN6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t0\t0\t2\t1\n+KIAA2013\t0\t0\t55\t1\t0\t0\t0\t0\t0\t0\t6\t0\t0\t0\t0\t0\t0\t43\t0\t0\n+PLOD1\t0\t0\t157\t108\t0\t134\t0\t0\t0\t215\t0\t32\t0\t0\t90\t95\t118\t0\t141\t216\n+MFN2\t3\t0\t0\t16\t0\t0\t0\t22\t0\t0\t0\t17\t18\t0\t0\t22\t0\t0\t0\t17\n+MIIP\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t9\n+TNFRSF8\t0\t0\t0\t14\t0\t0\t0\t0\t0\t3\t0\t0\t0\t4\t0\t22\t0\t0\t0\t0\n+TNFRSF1B\t0\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\t2\n+VPS13D\t0\t0\t0\t0\t0\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+DHRS3\t0\t0\t20\t46\t0\t0\t0\t0\t27\t0\t0\t0\t0\t0\t7\t0\t0\t8\t0\t54\n+PDPN\t0\t0\t30\t35\t0\t1\t10\t17\t0\t0\t28\t0\t15\t0\t0\t0\t36\t0\t0\t0\n+PRDM2\t0\t0\t0\t0\t4\t0\t0\t0\t0\t0\t0\t3\t0\t0\t0\t20\t0\t0\t6\t0\n+TMEM51\t43\t0\t38\t14\t0\t0\t60\t0\t0\t68\t0\t167\t116\t0\t0\t76\t30\t0\t0\t0\n+FHAD1\t0\t0\t457\t204\t111\t715\t255\t378\t0\t442\t0\t0\t226\t50\t0\t630\t330\t371\t0\t0\n+EFHD2\t125\t0\t152\t0\t137\t341\t0\t0\t0\t0\t296\t107\t416\t172\t265\t467\t471\t4\t0\t509\n+CASP9\t0\t0\t59\t126\t57\t0\t0\t30\t0\t0\t0\t0\t0\t0\t0\t0\t7\t138\t41\t79\n+DNAJC16\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t9\t0\t0\t0\t0\n+DDI2\t4\t0\t0\t0\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+RSC1A1\t5\t0\t0\t0\t0\t4\t0\t0\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\n+PLEKHM2\t0\t0\t30\t0\t0\t0\t0\t0\t0\t0\t8\t0\t0\t0\t0\t9\t0\t0\t0\t0\n+SLC25A34\t0\t0\t0\t0\t0\t0\t0\t5\t0\t0\t5\t39\t0\t0\t0\t12\t0\t0\t0\t0\n+FBLIM1\t0\t0\t0\t0\t0\t0\t13\t0\t0\t0\t0\t7\t19\t0\t0\t0\t0\t0\t0\t0\n+SPEN\t45\t4\t0\t154\t110\t0\t0\t31\t0\t0\t0\t0\t0\t0\t49\t0\t0\t124\t0\t27\n+ZBTB17\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t8\t0\t0\t0\t0\t0\t0\t0\t0\n+EPHA2\t8\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t8\t0\t0\t33\t0\t0\t0\t0\n+ARHGEF19\t0\t0\t0\t0\t0\t5\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t8\t0\t0\t0\n+FBXO42\t0\t0\t0\t0\t4\t0\t0\t5\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\n+SZRD1\t57\t28\t0\t0\t0\t0\t22\t0\t0\t0\t56\t71\t64\t0\t16\t0\t0\t0\t0\t0\n+NECAP2\t0\t0\t0\t0\t0\t10\t0\t0\t0\t0\t9\t9\t0\t0\t0\t0\t0\t10\t0\t2\n+CROCCP3\t0\t0\t0\t0\t0\t60\t0\t54\t0\t0\t64\t67\t107\t0\t0\t33\t0\t0\t0\t0\n+NBPF1\t0\t0\t0\t0\t0\t0\t4\t12\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t25\t8\n+CROCCP2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t1\t2\n+CROCC\t0\t0\t13\t25\t0\t19\t20\t0\t0\t24\t0\t0\t0\t0\t0\t0\t0\t0\t0\t19\n+ATP13A2\t0\t0\t0\t0\t35\t0\t0\t0\t0\t0\t45\t0\t0\t0\t0\t8\t0\t0\t0\t0\n+SDHB\t0\t157\t239\t0\t0\t71\t0\t0\t0\t0\t0\t22\t0\t0\t34\t147\t0\t0\t73\t247\n+PADI2\t0\t0\t0\t21\t0\t0\t8\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\n+PADI4\t0\t0\t0\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+RCC2\t0\t0\t44\t7\t8\t0\t0\t0\t0\t12\t0\t27\t0\t0\t12\t0\t0\t30\t0\t0\n+ARHGEF10L\t0\t0\t8\t0\t0\t0\t0\t0\t44\t0\t0\t0\t36\t0\t0\t0\t0\t0\t0\t0\n+IGSF21\t38\t0\t0\t0\t0\t117\t0\t0\t0\t53\t0\t123\t0\t0\t84\t136\t25\t0\t13\t0\n+ALDH4A1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t11\t0\t0\t0\t0\n+IFFO2\t0\t0\t0\t18\t70\t0\t85\t0\t37\t62\t0\t19\t0\t11\t0\t0\t11\t0\t0\t0\n+UBR4\t31\t136\t0\t28\t70\t0\t0\t0\t96\t43\t0\t52\t76\t125\t0\t0\t0\t0\t168\t88\n+EMC1\t5\t0\t0\t22\t15\t0\t0\t0\t0\t0\t0\t0\t6\t0\t0\t0\t0\t2\t5\t0\n+MRTO4\t0\t0\t0\t9\t0\t0\t0\t0\t11\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+AKR7A2\t0\t0\t0\t0\t62\t0\t0\t0\t3\t0\t0\t0\t0\t1\t0\t99\t39\t0\t15\t0\n+PQLC2\t0\t0\t0\t0\t0\t0\t0\t0\t11\t6\t0\t0\t0\t0\t0\t0\t0\t0\t7\t0\n+CAPZB\t0\t0\t0\t41\t0\t0\t0\t0\t21\t0\t0\t0\t0\t0\t2\t49\t0\t22\t3\t0\n+MINOS1\t0\t36\t0\t0\t21\t18\t0\t0\t27\t0\t0\t0\t18\t0\t0\t8\t0\t0\t17\t0\n+TMCO4\t0\t0\t4\t0\t0\t0\t0\t0\t24\t0\t4\t0\t32\t0\t0\t26\t0\t0\t0\t0\n+OTUD3\t0\t0\t0\t0\t0\t0\t4\t3\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\t0\t0\n+UBXN10\t0\t0\t173\t0\t165\t0\t0\t0\t0\t12\t89\t0\t74\t0\t29\t103\t0\t22\t0\t0\n+MUL1\t0\t7\t97\t66\t0\t0\t0\t0\t0\t93\t0\t68\t0\t144\t29\t0\t8\t81\t0\t0\n+CDA\t58\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t72\t0\t18\t81\t0\t0\t0\n+PINK1\t0\t6\t0\t3\t0\t0\t0\t0\t0\t0\t0\t8\t0\t0\t0\t0\t0\t0\t0\t0\n+DDOST\t0\t0\t0\t11\t80\t0\t0\t35\t58\t0\t67\t0\t117\t0\t0\t0\t0\t0\t0\t0\n+HP1BP3\t0\t0\t0\t6\t0\t0\t0\t0\t0\t7\t0\t1\t3\t8\t0\t0\t0\t0\t0\t0\n+EIF4G3\t0\t25\t50\t2\t0\t0\t0\t0\t0\t42\t0\t4\t0\t0\t11\t0\t0'..b'0\t0\t0\t0\t0\t0\t0\t0\t19\t0\t2\t3\t0\n+FAM199X\t0\t0\t0\t55\t17\t0\t0\t0\t0\t66\t0\t35\t0\t58\t17\t0\t0\t0\t0\t121\n+CXorf57\t0\t0\t0\t52\t0\t0\t0\t0\t0\t0\t0\t0\t0\t18\t0\t0\t0\t0\t0\t0\n+RNF128\t54\t0\t0\t0\t0\t167\t8\t0\t0\t0\t0\t0\t0\t283\t0\t0\t0\t0\t0\t221\n+TBC1D8B\t0\t0\t13\t40\t0\t0\t0\t0\t11\t0\t33\t0\t0\t0\t0\t0\t53\t8\t0\t0\n+MORC4\t0\t0\t0\t15\t0\t0\t0\t0\t3\t0\t0\t4\t0\t0\t0\t12\t0\t0\t3\t0\n+RBM41\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\n+PRPS1\t34\t0\t26\t0\t0\t0\t0\t0\t20\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\n+TSC22D3\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\n+MID2\t0\t0\t2\t1\t0\t0\t0\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\t0\t0\t0\n+VSIG1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t35\t0\t0\t0\t46\t0\n+PSMD10\t60\t0\t0\t5\t8\t0\t11\t0\t0\t0\t0\t0\t55\t0\t0\t53\t0\t0\t0\t14\n+ATG4A\t0\t0\t56\t0\t0\t36\t0\t0\t0\t46\t0\t0\t10\t0\t0\t0\t0\t9\t13\t2\n+NXT2\t23\t0\t0\t0\t0\t0\t0\t10\t8\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+ACSL4\t0\t0\t0\t0\t5\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\n+TMEM164\t0\t0\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\t5\t0\t0\t0\t0\t0\t0\t0\n+AMMECR1\t5\t0\t0\t0\t2\t0\t0\t0\t4\t9\t0\t11\t0\t0\t0\t8\t0\t0\t7\t0\n+ALG13\t0\t0\t0\t0\t39\t0\t0\t0\t17\t0\t5\t0\t48\t0\t0\t28\t14\t0\t48\t2\n+PLS3\t0\t4\t0\t0\t0\t0\t0\t0\t0\t0\t19\t0\t0\t0\t0\t0\t24\t0\t0\t0\n+WDR44\t0\t0\t20\t0\t0\t0\t0\t0\t0\t0\t47\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+DOCK11\t0\t12\t0\t0\t0\t15\t0\t0\t0\t0\t0\t0\t9\t0\t0\t0\t0\t5\t2\t0\n+IL13RA1\t0\t0\t36\t56\t37\t70\t0\t0\t0\t13\t0\t59\t0\t0\t17\t27\t0\t0\t0\t0\n+LONRF3\t13\t0\t0\t0\t0\t1\t0\t18\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t3\n+PGRMC1\t0\t29\t118\t14\t132\t155\t0\t207\t0\t0\t0\t0\t0\t0\t0\t0\t86\t0\t0\t57\n+SLC25A43\t22\t0\t0\t21\t4\t0\t0\t0\t0\t34\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\n+SLC25A5\t0\t0\t0\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\t0\t0\t10\t0\t0\t0\t0\n+CXorf56\t0\t0\t14\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5\t12\t0\t0\t15\t5\n+UBE2A\t59\t32\t0\t0\t21\t41\t18\t0\t0\t12\t0\t0\t5\t0\t0\t0\t0\t6\t46\t0\n+NKRF\t0\t7\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\n+SEPT6\t0\t1\t0\t0\t0\t0\t12\t0\t11\t6\t0\t0\t0\t0\t10\t21\t2\t0\t14\t23\n+RPL39\t26\t0\t9\t0\t61\t0\t35\t0\t21\t55\t0\t1\t0\t0\t49\t18\t0\t0\t0\t0\n+UPF3B\t0\t0\t24\t63\t0\t7\t0\t0\t0\t0\t0\t17\t23\t0\t0\t0\t0\t0\t0\t0\n+RNF113A\t0\t0\t0\t0\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\n+NDUFA1\t0\t0\t0\t0\t0\t29\t0\t0\t0\t0\t0\t0\t13\t20\t0\t0\t0\t0\t0\t22\n+NKAP\t0\t7\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+ZBTB33\t41\t0\t6\t0\t0\t0\t0\t0\t30\t0\t0\t0\t25\t0\t0\t57\t0\t0\t15\t0\n+LAMP2\t0\t0\t0\t0\t28\t0\t0\t0\t0\t0\t0\t0\t0\t16\t0\t0\t41\t0\t0\t0\n+CUL4B\t40\t0\t0\t0\t0\t0\t0\t75\t0\t31\t0\t0\t0\t0\t0\t45\t27\t35\t0\t0\n+MCTS1\t127\t0\t186\t0\t43\t46\t0\t158\t201\t0\t109\t0\t119\t135\t252\t0\t41\t0\t252\t32\n+C1GALT1C1\t12\t162\t0\t26\t0\t0\t0\t0\t22\t70\t54\t0\t38\t0\t113\t0\t4\t0\t0\t0\n+THOC2\t0\t0\t0\t0\t0\t3\t31\t0\t7\t0\t29\t0\t0\t5\t0\t0\t0\t16\t0\t26\n+XIAP\t210\t4\t0\t72\t81\t26\t0\t0\t0\t0\t0\t0\t0\t0\t32\t0\t0\t0\t0\t315\n+STAG2\t8\t0\t0\t0\t0\t0\t14\t13\t0\t0\t0\t0\t19\t0\t27\t7\t0\t8\t0\t48\n+SH2D1A\t0\t10\t0\t15\t0\t105\t0\t78\t104\t29\t167\t0\t0\t12\t0\t0\t23\t0\t6\t0\n+TENM1\t4\t0\t10\t0\t3\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5\n+SMARCA1\t37\t0\t93\t0\t0\t213\t0\t93\t18\t0\t156\t0\t86\t65\t0\t0\t0\t0\t45\t0\n+OCRL\t0\t0\t0\t0\t0\t0\t0\t8\t0\t0\t0\t17\t0\t0\t0\t0\t0\t0\t0\t1\n+APLN\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t0\t0\n+SASH3\t34\t113\t0\t0\t0\t94\t0\t0\t0\t0\t0\t0\t0\t0\t0\t194\t0\t54\t0\t0\n+ZDHHC9\t14\t0\t9\t0\t0\t0\t0\t19\t0\t0\t0\t0\t0\t0\t0\t21\t8\t0\t0\t0\n+UTP14A\t0\t1\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\n+BCORL1\t0\t0\t0\t0\t0\t6\t19\t0\t0\t2\t5\t0\t0\t0\t0\t0\t0\t5\t0\t16\n+ELF4\t0\t29\t5\t0\t0\t0\t0\t41\t0\t28\t0\t0\t0\t0\t0\t0\t0\t0\t32\t0\n+AIFM1\t194\t0\t80\t175\t0\t0\t43\t0\t85\t160\t3\t0\t71\t0\t0\t39\t0\t67\t0\t0\n+ZNF280C\t0\t0\t39\t41\t0\t14\t0\t0\t0\t0\t0\t0\t30\t28\t0\t2\t45\t0\t0\t0\n+SLC25A14\t0\t0\t0\t0\t0\t0\t33\t0\t0\t27\t30\t0\t0\t0\t0\t8\t0\t0\t0\t0\n+RBMX2\t0\t0\t0\t102\t0\t49\t147\t0\t233\t0\t0\t0\t0\t0\t114\t0\t67\t0\t0\t0\n+FAM45B\t0\t13\t0\t0\t0\t0\t0\t15\t0\t0\t8\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+ENOX2\t3\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+MST4\t0\t0\t0\t0\t17\t0\t0\t4\t14\t0\t4\t41\t0\t0\t0\t0\t13\t0\t13\t0\n+RAP2C\t0\t7\t19\t0\t0\t0\t0\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t46\t31\t0\n+MBNL3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t22\t12\t0\t0\t0\t0\t0\t16\n+GPC4\t0\t0\t0\t0\t5\t0\t42\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t25\t13\t0\n+GPC3\t5\t0\t0\t0\t0\t0\t0\t0\t0\t14\t0\t0\t0\t0\t0\t0\t12\t0\t0\t0\n+PHF6\t29\t0\t0\t14\t28\t0\t4\t0\t16\t0\t16\t24\t30\t0\t0\t0\t0\t0\t0\t24\n+HPRT1\t1\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t0\t0\t0\n+FAM122B\t30\t42\t0\t0\t0\t0\t0\t0\t0\t0\t9\t0\t42\t0\t1\t0\t0\t0\t0\t0\n+FAM122C\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t4\t0\t9\t5\t0\t0\t0\t0\t0\t0\n+MOSPD1\t3\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t16\t0\t11\t0\t0\t0\t0\t0\n+SMIM10\t18\t0\t0\t50\t0\t48\t0\t0\t0\t3\t0\t0\t0\t59\t0\t0\t0\t0\t0\t52\n+FAM127C\t0\t0\t41\t29\t0\t43\t0\t0\t79\t0\t0\t0\t0\t104\t0\t10\t0\t0\t85\t0\n+FAM127A\t0\t0\t0\t0\t30\t0\t0\t7\t75\t0\t0\t0\t41\t0\t0\t0\t8\t0\t15\t26\n+FAM127B\t0\t0\t7\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t3\t0\t0\t9\t0\t0\t4\n+ZNF75D\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t8\t0\t0\t0\n+USP9Y\t0\t27\t0\t1\t0\t38\t0\t41\t0\t0\t70\t35\t0\t0\t52\t0\t0\t0\t0\t0\n+DDX3Y\t0\t18\t0\t31\t0\t0\t0\t0\t0\t3\t6\t0\t0\t0\t0\t0\t0\t10\t0\t0\n+UTY\t0\t0\t29\t19\t0\t0\t0\t0\t1\t0\t0\t25\t0\t0\t0\t0\t20\t0\t0\t0\n+NLGN4Y\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\t0\t0\t0\t0\n'

diff -r 000000000000 -r be7c0c692879 test-data/test.gtf.gz

Binary file test-data/test.gtf.gz has changed