changeset 0:8745321ccc3e draft

planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
author lldelisle
date Mon, 24 Oct 2022 15:19:04 +0000
parents
children 3ff6eeca667e
files cooler_cload_tabix.xml macros.xml test-data/chr19.1M.bins test-data/chr19.size test-data/chrM.40kb.bins test-data/chrM.fa test-data/chrM.fa.fai test-data/fasta_indexes.loc test-data/input.cool test-data/input.validPairs.tabix test-data/input.validPairs.tabix.tbi test-data/input.validPairs.txt test-data/output.cool tool-data/fasta_indexes.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test workflow_cooler.pdf
diffstat 17 files changed, 20556 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cooler_cload_tabix.xml	Mon Oct 24 15:19:04 2022 +0000
@@ -0,0 +1,71 @@
+<tool id="cooler_cload_tabix" name="cooler_cload_tabix" version="@VERSION@+galaxy0" profile="18.01">
+  <description> Create a cool file from a tabix-indexed contact file and a list of genomic bins.</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <expand macro="stdio" />
+  <command detect_errors="exit_code"><![CDATA[
+    ##set up input files
+    ln -s '$input_pairs' pairs.tabix &&
+    #if str( $input_pairs.metadata.tabix_index ) != "None":
+      ln -s '$input_pairs.metadata.tabix_index' pairs.tabix.tbi &&
+    #else:
+      tabix -s $pairs_advanced.c1 -b $pairs_advanced.p1 -e $pairs_advanced.p1 pairs.tabix &&
+    #end if
+    cooler cload tabix --assembly '$assembly' -c2 $c2 -p2 $p2 '$input_bed' pairs.tabix '$output'
+    ]]>
+  </command>
+  <inputs>
+    <param name="input_pairs" multiple="false"  type="data" format="bgzip,tabix" label="Select the output of csort_tabix."/>
+    <section name="pairs_advanced" title="If your input is not already indexed" expanded="False">
+      <param name="c1" type="integer" value="1" label="field number in the input file (starting from 1) of the chromosome of mate 1.">
+        <validator type="in_range" min="1" />
+      </param>
+      <param name="p1" type="integer" value="2" label="field number in the input file (starting from 1) of the position of mate 1.">
+        <validator type="in_range" min="1" />
+      </param>
+    </section>
+    <param name="c2" type="integer" value="3" label="field number in the input file (starting from 1) of the chromosome of mate 2 (same as in csort).">
+      <validator type="in_range" min="1" />
+    </param>
+    <param name="p2" type="integer" value="4" label="field number in the input file (starting from 1) of the position of mate 2 (same as in csort).">
+      <validator type="in_range" min="1" />
+    </param>
+    <param name="assembly" type="text" label="name of genome assembly"/>
+    <param name="input_bed" multiple="false"  type="data" format="bed" label="Select the output of makebins."/>
+  </inputs>
+  
+  <outputs>
+    <data format="cool" name="output" label="cool file from $input_pairs.name and $input_bed.name"/>
+  </outputs>
+  
+  <tests>
+    <!-- For the moment I cannot test this tool -->
+    <!-- <test>
+      <param name="input_pairs" value="input.validPairs.tabix" ftype="bgzip"/>
+      <param name="input_bed" value="chr19.1M.bins"/>
+      <param name="assembly" value="chr19"/>
+      <section name="pairs_advanced">
+        <param name="c1" value="3"/>
+        <param name="p1" value="4"/>
+      </section>
+      <param name="c2" value="7"/>
+      <param name="p2" value="8"/>
+      <output name="output" file="input.cool" compare="sim_size"/>
+    </test> -->
+  </tests> 
+
+  <help>
+    **cooler cload**
+    tool developped by mirnylab
+    see https://github.com/open2c/cooler
+    and https://cooler.readthedocs.io/en/latest/cli.html#cooler-cload-tabix
+        
+    command-line::
+    
+      cooler cload tabix --assembly assembly -c2 c2 -p2 p2 input_bed input_pairs output
+    
+  </help>
+  <expand macro="citation_cooler" />
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Oct 24 15:19:04 2022 +0000
@@ -0,0 +1,44 @@
+<macros>
+  <token name="@VERSION@">0.8.11</token>
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="1.16">htslib</requirement>
+      <requirement type="package" version="3.7.0">h5py</requirement>
+      <requirement type="package" version="@VERSION@">cooler</requirement>
+    </requirements>
+  </xml>
+  <xml name="stdio">
+    <stdio>
+      <!-- Anything other than zero is an error -->
+      <exit_code range="1:" />
+      <exit_code range=":-1" />
+      <!-- In case the return code has not been set propery check stderr too -->
+      <regex match="Error:" />
+      <regex match="Exception:" />
+    </stdio>
+    <version_command>cooler --version</version_command>
+  </xml>
+  <xml name="size_macro">
+    <conditional name="size_source">
+      <param name="size_source_selector" type="select" label="Choose the source for the chromosome sizes">
+          <option value="cached">Locally cached</option>
+          <option value="history">History</option>
+      </param>
+      <when value="cached">
+          <param name="fasta_cached" type="select" label="Fasta availables">
+              <options from_data_table="fasta_indexes">
+                  <validator type="no_options" message="No cached fasta is available"/>
+              </options>
+          </param>
+      </when>
+      <when value="history">
+        <param name="chromosomeSize" multiple="false" type="data" format="tabular" label="Select a file with the size of chromosome (One column with the chromosome names in the desired order, one column with the sizes)."/>
+      </when>
+    </conditional>
+  </xml>
+  <xml name="citation_cooler">
+      <citations>
+          <citation type="doi">10.1093/bioinformatics/btz540</citation>
+      </citations>
+  </xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chr19.1M.bins	Mon Oct 24 15:19:04 2022 +0000
@@ -0,0 +1,62 @@
+chr19	0	1000000
+chr19	1000000	2000000
+chr19	2000000	3000000
+chr19	3000000	4000000
+chr19	4000000	5000000
+chr19	5000000	6000000
+chr19	6000000	7000000
+chr19	7000000	8000000
+chr19	8000000	9000000
+chr19	9000000	10000000
+chr19	10000000	11000000
+chr19	11000000	12000000
+chr19	12000000	13000000
+chr19	13000000	14000000
+chr19	14000000	15000000
+chr19	15000000	16000000
+chr19	16000000	17000000
+chr19	17000000	18000000
+chr19	18000000	19000000
+chr19	19000000	20000000
+chr19	20000000	21000000
+chr19	21000000	22000000
+chr19	22000000	23000000
+chr19	23000000	24000000
+chr19	24000000	25000000
+chr19	25000000	26000000
+chr19	26000000	27000000
+chr19	27000000	28000000
+chr19	28000000	29000000
+chr19	29000000	30000000
+chr19	30000000	31000000
+chr19	31000000	32000000
+chr19	32000000	33000000
+chr19	33000000	34000000
+chr19	34000000	35000000
+chr19	35000000	36000000
+chr19	36000000	37000000
+chr19	37000000	38000000
+chr19	38000000	39000000
+chr19	39000000	40000000
+chr19	40000000	41000000
+chr19	41000000	42000000
+chr19	42000000	43000000
+chr19	43000000	44000000
+chr19	44000000	45000000
+chr19	45000000	46000000
+chr19	46000000	47000000
+chr19	47000000	48000000
+chr19	48000000	49000000
+chr19	49000000	50000000
+chr19	50000000	51000000
+chr19	51000000	52000000
+chr19	52000000	53000000
+chr19	53000000	54000000
+chr19	54000000	55000000
+chr19	55000000	56000000
+chr19	56000000	57000000
+chr19	57000000	58000000
+chr19	58000000	59000000
+chr19	59000000	60000000
+chr19	60000000	61000000
+chr19	61000000	61431566
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chr19.size	Mon Oct 24 15:19:04 2022 +0000
@@ -0,0 +1,1 @@
+chr19	61431566
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chrM.40kb.bins	Mon Oct 24 15:19:04 2022 +0000
@@ -0,0 +1,1 @@
+chrM	0	16569
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chrM.fa	Mon Oct 24 15:19:04 2022 +0000
@@ -0,0 +1,333 @@
+>chrM
+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCAT
+TTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTG
+GAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATC
+CTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTA
+AAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAACAATTGAAT
+GTCTGCACAGCCACTTTCCACACAGACATCATAACAAAAAATTTCCACCA
+AACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA
+AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTT
+TATCTTTTGGCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATT
+ATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATACAACCCCCGC
+CCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCA
+ACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAA
+GCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAAAT
+AGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA
+GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGA
+ACAAGCATCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCAC
+ACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTT
+AACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGC
+GGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTA
+GATCACCCCCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACT
+CCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC
+ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCC
+TAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAGAACACTACGAGC
+CACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGAGG
+AGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTC
+AGCCTATATACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAA
+GCGCAAGTACCCACGTAAAGACGTTAGGTCAAGGTGTAGCCCATGAGGTG
+GCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT
+GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGC
+TTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCCTC
+AAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATAGA
+GGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAA
+CCAGAGTGTAGCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCA
+ACTTAACTTGACCGCTCTGAGCTAAACCTAGCCCCAAACCCACTCCACCT
+TACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG
+ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATG
+AAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTCT
+GCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGA
+CCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGT
+CTATGTAGCAAAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTAC
+CGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTTAGTTCAACTTTA
+AATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC
+CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGT
+AAAAAATTTAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGAAA
+GCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAACATATAACTGA
+ACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATG
+TTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGA
+TTAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCAAC
+AAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA
+AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTA
+CCAAAAACATCACCTCTAGCATCACCAGTATTAGAGGCACCGCCTGCCCA
+GTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAaaggtagcata
+atcacttgttccttaaatagggacctgtatgaatggctccacgagggttc
+agctgtctcttacttttaaccagtgaaattgacctgcccgtgaagaggcg
+ggcataacacagcaagacgagaagaccctatggagctttaatttaTTAAT
+GCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT
+AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGT
+ACATGCTAAGACTTCACCAGTCAAAGCGAACTACTATACTCAATTGATCC
+AATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACAGCGCAATCCT
+ATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCA
+GGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATT
+AAAGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCT
+ATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT
+ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATT
+ATACCCACACCCACCCAAGAACAGGGTTTgttaagatggcagagcccggt
+aatcgcataaaacttaaaactttacagtcagaggttcaattcctcttctt
+aacaacaTACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAAT
+CGCAATGGCATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATAC
+AACTACGCAAAGGCCCCAACGTTGTAGGCCCCTACGGGCTACTACAACCC
+TTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC
+ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCG
+CTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACCTC
+AACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACTC
+AATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCG
+CACTGCGAGCAGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATC
+ATTCTACTATCAACATTACTAATAAGTGGCTCCTTTAACCTCTCCACCCT
+TATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGG
+CCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCTTC
+GACCTTGCCGAAGGGGAGTCCGAACTAGTCTCAGGCTTCAACATCGAATA
+CGCCGCAGGCCCCTTCGCCCTATTCTTCATAGCCGAATACACAAACATTA
+TTATAATAAACACCCTCACCACTACAATCTTCCTAGGAACAACATATGAC
+GCACTCTCCCCTGAACTCTACACAACATATTTTGTCACCAAGACCCTACT
+TCTAACCTCCCTGTTCTTATGAATTCGAACAGCATACCCCCGATTCCGCT
+ACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCCTA
+GCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCC
+CCCTCAAACCTAAGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTA
+AATAATAGGAGCTTAAACCCCCTTATTTctaggactatgagaatcgaacc
+catccctgagaatccaaaattctccgtgccacctatcacaccccatccta
+AAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGG
+TTATACCCTTCCCGTACTAATTAATCCCCTGGCCCAACCCGTCATCTACT
+CTACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTT
+TTTACCTGAGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTCT
+AACCAAAAAAATAAACCCTCGTTCCACAGAAGCTGCCATCAAGTATTTCC
+TCACGCAAGCAACCGCATCCATAATCCTTCTAATAGCTATCCTCTTCAAC
+AATATACTCTCCGGACAATGAACCATAACCAATACTACCAATCAATACTC
+ATCATTAATAATCATAATAGCTATAGCAATAAAACTAGGAATAGCCCCCT
+TTCACTTCTGAGTCCCAGAGGTTACCCAAGGCACCCCTCTGACATCCGGC
+CTGCTTCTTCTCACATGACAAAAACTAGCCCCCATCTCAATCATATACCA
+AATCTCTCCCTCACTAAACGTAAGCCTTCTCCTCACTCTCTCAATCTTAT
+CCATCATAGCAGGCAGTTGAGGTGGATTAAACCAAACCCAGCTACGCAAA
+ATCTTAGCATACTCCTCAATTACCCACATAGGATGAATAATAGCAGTTCT
+ACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTATCC
+TAACTACTACCGCATTCCTACTACTCAACTTAAACTCCAGCACCACGACC
+CTACTACTATCTCGCACCTGAAACAAGCTAACATGACTAACACCCTTAAT
+TCCATCCACCCTCCTCTCCCTAGGAGGCCTGCCCCCGCTAACCGGCTTTT
+TGCCCAAATGGGCCATTATCGAAGAATTCACAAAAAACAATAGCCTCATC
+ATCCCCACCATCATAGCCACCATCACCCTCCTTAACCTCTACTTCTACCT
+ACGCCTAATCTACTCCACCTCAATCACACTACTCCCCATATCTAACAACG
+TAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCCC
+ACACTCATCGCCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATACT
+AATAATCTTATAGAAATTTAGGTTAAATACAGACCAAGAGCCTTCAAAGC
+CCTCAGTAAGTTGCAATACTTAATTTCTGTAACAGCTAAGGACTGCAAAA
+CCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAG
+CCCTTACTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGCT
+AAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCCGCCGGGAAAA
+AAGGCGGGAGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAA
+TTCAATATGAAAATCACCTCGGAGCTGGTAAAAAGAGGCCTAACCCCTGT
+CTTTAGATTTACAGTCCAATGCTTCACTCAGCCATTTTACCTCACCCCCA
+CTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCACAAAGACATTGG
+AACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCTC
+TAAGCCTCCTTATTCGAGCCGAGCTGGGCCAGCCAGGCAACCTTCTAGGT
+AACGACCACATCTACAACGTTATCGTCACAGCCCATGCATTTGTAATAAT
+CTTCTTCATAGTAATACCCATCATAATCGGAGGCTTTGGCAACTGACTAG
+TTCCCCTAATAATCGGTGCCCCCGATATGGCGTTTCCCCGCATAAACAAC
+ATAAGCTTCTGACTCTTACCTCCCTCTCTCCTACTCCTGCTCGCATCTGC
+TATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTTAG
+CAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCC
+TTACACCTAGCAGGTGTCTCCTCTATCTTAGGGGCCATCAATTTCATCAC
+AACAATTATCAATATAAAACCCCCTGCCATAACCCAATACCAAACGCCCC
+TCTTCGTCTGATCCGTCCTAATCACAGCAGTCCTACTTCTCCTATCTCTC
+CCAGTCCTAGCTGCTGGCATCACTATACTACTAACAGACCGCAACCTCAA
+CACCACCTTCTTCGACCCCGCCGGAGGAGGAGACCCCATTCTATACCAAC
+ACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACCA
+GGCTTCGGAATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAGA
+ACCATTTGGATACATAGGTATGGTCTGAGCTATGATATCAATTGGCTTCC
+TAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGGAATAGACGTA
+GACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCAC
+CGGCGTCAAAGTATTTAGCTGACTCGCCACACTCCACGGAAGCAATATGA
+AATGATCTGCTGCAGTGCTCTGAGCCCTAGGATTCATCTTTCTTTTCACC
+GTAGGTGGCCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGT
+ACTACACGACACGTACTACGTTGTAGCCCACTTCCACTATGTCCTATCAA
+TAGGAGCTGTATTTGCCATCATAGGAGGCTTCATTCACTGATTTCCCCTA
+TTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAATCCATTTCACTAT
+CATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGGCC
+TATCCGGAATGCCCCGACGTTACTCGGACTACCCCGATGCATACACCACA
+TGAAACATCCTATCATCTGTAGGCTCATTCATTTCTCTAACAGCAGTAAT
+ATTAATAATTTTCATGATTTGAGAAGCCTTCGCTTCGAAGCGAAAAGTCC
+TAATAGTAGAAGAACCCTCCATAAACCTGGAGTGACTATATGGATGCCCC
+CCACCCTACCACACATTCGAAGAACCCGTATACATAAAATCTAGACAaaa
+aaggaaggaatcgaaccccccaaagctggtttcaagccaaccccatggcc
+tccatgactttttcAAAAAGGTATTAGAAAAACCATTTCATAACTTTGTC
+AAAGTTAAATTATAGGCTAAATCCTATATATCTTAATGGCACATGCAGCG
+CAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTTATCAC
+CTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCC
+TGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATC
+TCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCAT
+CCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGACG
+AGGTCAACGATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTAC
+TGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCCTACAT
+ACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGACTCCTTGACGTTG
+ACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACA
+TCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAAC
+AGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGAC
+CGGGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAGT
+TTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATAGG
+GCCCGTATTTACCCTATAGCACCCCCTCTACCCCCTCTAGAGCCCACTGT
+AAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAACA
+CCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACCAT
+AATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATAT
+TAAACACAAACTACCACCTACCTCCCTCACCAAAGCCCATAAAAATAAAA
+AATTATAACAAACCCTGAGAACCAAAATGAACGAAAATCTGTTCGCTTCA
+TTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCAGTACTGATCATTCT
+ATTTCCCCCTCTATTGATCCCCACCTCCAAATATCTCATCAACAACCGAC
+TAATCACCACCCAACAATGACTAATCAAACTAACCTCAAAACAAATGATA
+ACCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTT
+AATCATTTTTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCAT
+TTACACCAACCACCCAACTATCTATAAACCTAGCCATGGCCATCCCCTTA
+TGAGCGGGCACAGTGATTATAGGCTTTCGCTCTAAGATTAAAAATGCCCT
+AGCCCACTTCTTACCACAAGGCACACCTACACCCCTTATCCCCATACTAG
+TTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTA
+CGCCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTAATTGG
+AAGCGCCACCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCA
+TCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCTTA
+ATCCAAGCCTACGTTTTCACACTTCTAGTAAGCCTCTACCTGCACGACAA
+CACATAATGACCCACCAATCACATGCCTATCATATAGTAAAACCCAGCCC
+ATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTAG
+CCATGTGATTTCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTA
+ACCAACACACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAG
+CACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATACG
+GGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTTC
+TGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCAATTAGGAGGGCA
+CTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAAGTCCCACTCC
+TAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCAC
+CATAGTCTAATAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTAT
+TACAATTTTACTGGGTCTCTATTTTACCCTCCTACAAGCCTCAGAGTACT
+TCGAGTCTCCCTTCACCATTTCCGACGGCATCTACGGCTCAACATTTTTT
+GTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGGCTCAACTTTCCT
+CACTATCTGCTTCATCCGCCAACTAATATTTCACTTTACATCCAAACATC
+ACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGTAGATGTGGTT
+TGACTATTTCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTAG
+TATAAATAGTACCGTTAACTTCCAATTAACTAGTTTTGACAACATTCAAA
+AAAGAGTAATAAACTTCGCCTTAATTTTAATAATCAACACCCTCCTAGCC
+TTACTACTAATAATTATTACATTTTGACTACCACAACTCAACGGCTACAT
+AGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGCCC
+GCGTCCCTTTCTCCATAAAATTCTTCTTAGTAGCTATTACCTTCTTATTA
+TTTGATCTAGAAATTGCCCTCCTTTTACCCCTACCATGAGCCCTACAAAC
+AACTAACCTGCCACTAATAGTTATGTCATCCCTCTTATTAATCATCATCC
+TAGCCCTAAGTCTGGCCTATGAGTGACTACAAAAAGGATTAGACTGAACC
+GAATTGGTATATAGTTTAAACAAAACGAATGATTTCGACTCATTAAATTA
+TGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACTAG
+CATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATA
+TCCTCCCTACTATGCCTAGAAGGAATAATACTATCGCTGTTCATTATAGC
+TACTCTCATAACCCTCAACACCCACTCCCTCTTAGCCAATATTGTGCCTA
+TTGCCATACTAGTCTTTGCCGCCTGCGAAGCAGCGGTGGGCCTAGCCCTA
+CTAGTCTCAATCTCCAACACATATGGCCTAGACTACGTACATAACCTAAA
+CCTACTCCAATGCTAAAACTAATCGTCCCAACAATTATATTACTACCACT
+GACATGACTTTCCAAAAAACACATAATTTGAATCAACACAACCACCCACA
+GCCTAATTATTAGCATCATCCCTCTACTATTTTTTAACCAAATCAACAAC
+AACCTATTTAGCTGTTCCCCAACCTTTTCCTCCGACCCCCTAACAACCCC
+CCTCCTAATACTAACTACCTGACTCCTACCCCTCACAATCATGGCAAGCC
+AACGCCACTTATCCAGTGAACCACTATCACGAAAAAAACTCTACCTCTCT
+ATACTAATCTCCCTACAAATCTCCTTAATTATAACATTCACAGCCACAGA
+ACTAATCATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCTTGG
+CTATCATCACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACA
+TACTTCCTATTCTACACCCTAGTAGGCTCCCTTCCCCTACTCATCGCACT
+AATTTACACTCACAACACCCTAGGCTCACTAAACATTCTACTACTCACTC
+TCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAACTTAATATGACTA
+GCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCACTT
+ATGACTCCCTAAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTAC
+TTGCCGCAGTACTCTTAAAACTAGGCGGCTATGGTATAATACGCCTCACA
+CTCATTCTCAACCCCCTGACAAAACACATAGCCTACCCCTTCCTTGTACT
+ATCCCTATGAGGCATAATTATAACAAGCTCCATCTGCCTACGACAAACAG
+ACCTAAAATCGCTCATTGCATACTCTTCAATCAGCCACATAGCCCTCGTA
+GTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAGTCAT
+TCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAA
+ACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGA
+CTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCT
+CGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTG
+TGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGA
+CTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAAC
+ACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCA
+CACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTA
+TCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTT
+AACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTACGACCCCTTA
+TTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCCCCCATGTCTAAC
+AACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAG
+GCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACAC
+TACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCA
+CCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCC
+ATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCAT
+GTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCC
+AAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAATA
+TTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACT
+GTGATATATAAACTCAGACCCAAACATTAATCAGTTCTTCAAATATCTAC
+TCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAACAACCTATTC
+CAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCAT
+CAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAA
+TCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCATGA
+TTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA
+CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAG
+GCAAATCAGCCCAATTAGGTCTCCACCCCTGACTCCCCTCAGCCATAGAA
+GGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTATAGTTGTAGC
+AGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCAC
+TAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCA
+GCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCTC
+CACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC
+CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATA
+CTATTTATGTGCTCCGGGTCCATCATCCACAACCTTAACAATGAACAAGA
+TATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTCACTTCAACCT
+CCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGT
+TTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAAA
+CGCCTGAGCCCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCCT
+ATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC
+ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAA
+ACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCATTACTAACAACA
+TTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAACTC
+ACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAA
+CTACCTAACCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTATT
+TCTCCAACATACTCGGATTCTACCCTAGCATCACACACCGCACAATCCCC
+TATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT
+AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCT
+CCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACTTC
+CTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAATCACATAACC
+TATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTT
+CAACCAGTAACTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGC
+ACCAATAGGATCCTCCCGAATCAACCCTGACCCCTCTCCTTCATAAATTA
+TTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC
+TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAAC
+ACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCAA
+TAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATAA
+ATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAAT
+AACACACCCGACCACACCGCTAACAATCAATACTAAACCCCCATAAATAG
+GAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACTAAACCCACACTC
+AACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC
+CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGA
+CCCCAATACGCAAAACTAACCCCCTAATAAAATTAATTAACCACTCATTC
+ATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAAACTTCGGCTC
+ACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAG
+CCATGCACTACTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCAC
+ATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCCAA
+TGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC
+TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATC
+CTCCTGCTTGCAACTATAGCAACAGCCTTCATAGGCTATGTCCTCCCGTG
+AGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAACTTACTATCCG
+CCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTAC
+TCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTT
+GCCCTTCATTATTGCAGCCCTAGCAACACTCCACCTCCTATTCTTGCACG
+AAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC
+ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTT
+CCTTCTCTCCTTAATGACATTAACACTATTCTCACCAGACCTCCTAGGCG
+ACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCCTCCCCACATC
+AAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCC
+TAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAG
+CAATAATCCCCATCCTCCATATATCCAAACAACAAAGCATAATATTTCGC
+CCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT
+AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGAC
+AAGTAGCATCCGTACTATACTTCACAACAATCCTAATCCTAATACCAACT
+ATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGTAT
+AAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGG
+ACAAATCAGAGAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAG
+ATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGT
+ACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA
+TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCAC
+CTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCTCCCCATGCTTA
+CAAGcaagtacagcaatcaaccctcaactatcacacatcaactgcaactC
+CAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAA
+CAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAA
+ATCCCTTCTCGTCCCCATGGATGACCCCCCTCAGATAGGGGTCCCTTGAC
+CACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG
+CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACAT
+CTGGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCT
+TAAATAAGACATCACGATG
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chrM.fa.fai	Mon Oct 24 15:19:04 2022 +0000
@@ -0,0 +1,1 @@
+chrM	16569	6	50	51
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_indexes.loc	Mon Oct 24 15:19:04 2022 +0000
@@ -0,0 +1,1 @@
+chrM	hg19	human mitochondrial genome	${__HERE__}/chrM.fa
Binary file test-data/input.cool has changed
Binary file test-data/input.validPairs.tabix has changed
Binary file test-data/input.validPairs.tabix.tbi has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.validPairs.txt	Mon Oct 24 15:19:04 2022 +0000
@@ -0,0 +1,20000 @@
+83	0	chr19	23041923	6434	0	chr19	22468767	6238	42	42
+177	0	chr19	7494919	1129	1	chr19	7590087	1161	42	40
+197	0	chr19	46286176	13818	0	chr19	46765336	13943	42	42
+288	0	chr19	36244729	10819	0	chr19	36745142	10979	42	42
+458	0	chr19	32210012	9428	1	chr19	36832116	11004	42	34
+601	0	chr19	3909853	271	1	chr19	3922275	277	42	42
+602	0	chr19	25351870	7147	1	chr19	25376235	7154	42	42
+711	0	chr19	28229621	8128	0	chr19	27983277	8051	42	42
+775	0	chr19	40964930	12289	1	chr19	41036736	12313	42	42
+782	1	chr19	41390888	12410	1	chr19	34916158	10345	42	42
+830	0	chr19	5802570	767	1	chr19	5605692	722	42	42
+871	0	chr19	21406650	5899	1	chr19	21534141	5936	42	42
+949	0	chr19	19843854	5329	1	chr19	19839772	5326	42	42
+1043	1	chr19	27439787	7847	1	chr19	27577107	7901	42	42
+1131	1	chr19	5100343	603	1	chr19	4752092	472	42	42
+1257	1	chr19	38049729	11386	0	chr19	37952044	11358	42	42
+1420	0	chr19	10387209	2112	1	chr19	10400249	2115	42	42
+1481	0	chr19	45074815	13468	1	chr19	44795267	13402	42	42
+1690	0	chr19	34494677	10211	1	chr19	32162326	9414	42	42
+1717	0	chr19	47913242	14247	0	chr19	48200469	14329	42	40
+1768	1	chr19	26477924	7505	1	chr19	26542344	7527	42	42
+2197	1	chr19	10909784	2240	0	chr19	10805735	2212	42	42
+2231	0	chr19	8665734	1549	1	chr19	3467945	134	42	42
+2357	0	chr19	5996648	817	0	chr19	6295093	887	42	42
+2728	0	chr19	32364510	9484	0	chr19	11938051	2597	23	42
+2795	1	chr19	22093986	6123	1	chr19	22039985	6107	42	42
+3101	0	chr19	49834691	14870	0	chr19	49349403	14704	42	42
+3138	0	chr19	18945080	4997	0	chr19	18996422	5019	42	42
+3210	1	chr19	44146243	13204	1	chr19	43554061	13049	40	42
+3532	0	chr19	18795442	4938	0	chr19	17264367	4431	42	42
+3846	1	chr19	26373848	7460	1	chr19	29141130	8443	42	42
+3950	1	chr19	46286176	13818	1	chr19	10553114	2141	42	42
+4102	1	chr19	14529186	3465	0	chr19	14709502	3534	42	42
+4207	0	chr19	29304304	8496	1	chr19	29247860	8474	42	42
+4264	1	chr19	10450271	2123	1	chr19	10383171	2111	42	42
+4631	1	chr19	24330813	6851	0	chr19	19049871	5045	42	42
+4867	1	chr19	31911918	9319	1	chr19	20856791	5699	42	42
+5101	1	chr19	16516055	4169	0	chr19	16430755	4146	42	42
+5231	1	chr19	42094834	12604	1	chr19	42087964	12598	42	42
+5258	0	chr19	28281552	8146	0	chr19	31338426	9149	42	42
+5315	0	chr19	17142848	4392	0	chr19	17210309	4411	42	42
+5342	1	chr19	38776630	11611	1	chr19	34816725	10315	42	42
+5499	1	chr19	46086483	13757	1	chr19	46943336	13991	40	42
+5585	1	chr19	44387343	13282	0	chr19	45078127	13471	42	42
+5596	1	chr19	8886188	1605	0	chr19	9010852	1633	42	42
+5836	1	chr19	47628422	14164	1	chr19	47135679	14036	42	42
+6108	0	chr19	38039057	11384	0	chr19	37706566	11273	8	42
+6195	1	chr19	42623198	12761	1	chr19	43393936	13002	42	40
+6480	0	chr19	34991110	10373	0	chr19	3756175	211	42	42
+6552	0	chr19	38676177	11579	1	chr19	38716449	11596	42	35
+6571	0	chr19	29275366	8482	1	chr19	23110150	6456	40	42
+6756	1	chr19	41000059	12306	0	chr19	7299136	1075	42	42
+6771	0	chr19	21451274	5912	1	chr19	49380031	14716	42	42
+6932	0	chr19	11399388	2407	1	chr19	11783418	2542	42	42
+6946	0	chr19	22597466	6290	0	chr19	22499051	6255	42	40
+7152	1	chr19	45904492	13702	0	chr19	18900938	4980	42	42
+7201	1	chr19	21160025	5818	1	chr19	11873008	2575	40	42
+7211	1	chr19	16140612	4030	1	chr19	23911601	6740	42	42
+7327	1	chr19	28184231	8112	1	chr19	28539598	8236	42	42
+7598	0	chr19	6677330	973	0	chr19	6667956	970	42	42
+7758	1	chr19	33262507	9803	1	chr19	33034504	9724	42	39
+7835	0	chr19	44587914	13344	0	chr19	43786819	13106	42	42
+8055	0	chr19	32076137	9380	1	chr19	32121774	9401	42	42
+8131	0	chr19	15906103	3948	1	chr19	15909954	3950	42	0
+8534	0	chr19	42251250	12645	0	chr19	41290915	12378	42	42
+8764	1	chr19	16378883	4135	0	chr19	16326023	4112	42	42
+9221	1	chr19	34478986	10201	0	chr19	36759311	10983	23	42
+9376	1	chr19	37424513	11194	0	chr19	15614447	3853	42	42
+9538	0	chr19	46833110	13956	1	chr19	47267243	14072	8	40
+9645	1	chr19	45494147	13595	1	chr19	45487608	13592	42	42
+9662	1	chr19	28527330	8233	0	chr19	27562159	7895	42	39
+9896	0	chr19	20843774	5692	0	chr19	20778038	5664	3	42
+10009	0	chr19	33000121	9703	0	chr19	33023502	9717	42	40
+10114	1	chr19	30881444	9016	1	chr19	20227569	5448	42	42
+10152	1	chr19	30489968	8886	0	chr19	32638640	9571	42	40
+10375	1	chr19	17893587	4628	1	chr19	17679986	4551	42	40
+10380	1	chr19	4244428	356	0	chr19	4277085	360	42	42
+10415	0	chr19	23446785	6570	0	chr19	32719596	9599	42	42
+10428	0	chr19	47205312	14058	0	chr19	45815193	13675	42	42
+10543	0	chr19	17033110	4347	0	chr19	16777964	4256	24	42
+10679	1	chr19	25854736	7293	1	chr19	26589536	7541	42	42
+11054	1	chr19	22077955	6116	0	chr19	22139690	6136	42	42
+11183	1	chr19	42943023	12856	1	chr19	42950901	12859	42	42
+11315	0	chr19	7022465	1013	0	chr19	16995393	4334	42	42
+11331	1	chr19	28072888	8083	0	chr19	28079965	8088	42	42
+11382	0	chr19	33314192	9822	0	chr19	33326622	9829	42	42
+11473	0	chr19	24427292	6881	0	chr19	23078774	6446	42	42
+11520	1	chr19	37218900	11132	1	chr19	36237813	10817	42	42
+11526	0	chr19	27181058	7749	1	chr19	27111314	7726	42	42
+11589	1	chr19	26877780	7643	1	chr19	26939509	7658	42	42
+11781	1	chr19	28826207	8330	0	chr19	26898940	7648	42	42
+11871	1	chr19	37266517	11144	0	chr19	37074904	11089	42	42
+11946	0	chr19	44084898	13185	1	chr19	44119792	13195	42	42
+12146	1	chr19	22484847	6250	1	chr19	29854632	8681	42	42
+12295	0	chr19	18001120	4665	1	chr19	17485191	4478	42	23
+12352	1	chr19	33450357	9868	0	chr19	36404269	10864	35	42
+12375	1	chr19	32973130	9693	0	chr19	33057983	9737	42	42
+12405	1	chr19	4924950	559	0	chr19	6660169	969	42	42
+12435	0	chr19	33942585	10025	1	chr19	18662512	4897	42	42
+12531	0	chr19	29832506	8669	1	chr19	32761311	9622	42	42
+12651	1	chr19	20439814	5528	0	chr19	21476594	5920	42	42
+12729	1	chr19	48550935	14447	0	chr19	42496636	12715	42	23
+12983	1	chr19	40958497	12288	0	chr19	40969570	12290	42	36
+13011	1	chr19	43718884	13083	0	chr19	43786819	13106	42	42
+13266	0	chr19	27995902	8056	0	chr19	28745640	8309	42	42
+13442	0	chr19	35753059	10652	1	chr19	35886571	10703	42	42
+13575	1	chr19	45504551	13600	0	chr19	45498035	13598	42	42
+13655	1	chr19	30784701	8972	0	chr19	31533533	9202	42	34
+13763	0	chr19	44784574	13399	1	chr19	42150154	12622	40	42
+13802	0	chr19	23250684	6500	1	chr19	42066941	12588	42	42
+13900	0	chr19	4917018	557	0	chr19	4358376	379	42	42
+14333	1	chr19	9163915	1676	1	chr19	11612126	2484	42	42
+14375	1	chr19	24351637	6857	0	chr19	40466572	12136	42	42
+14544	0	chr19	36146121	10792	0	chr19	33668905	9937	42	39
+14596	1	chr19	37302141	11156	1	chr19	34777956	10297	42	24
+14727	1	chr19	46165986	13772	0	chr19	46159391	13770	40	42
+14799	0	chr19	20984182	5748	1	chr19	18745562	4919	39	42
+14833	0	chr19	31211558	9105	1	chr19	32677910	9585	42	42
+15084	0	chr19	8831505	1591	1	chr19	8917776	1613	23	42
+15242	0	chr19	29836939	8673	0	chr19	43812834	13113	42	42
+15280	0	chr19	28797811	8324	1	chr19	28420681	8204	42	42
+15705	0	chr19	12517282	2778	0	chr19	11809627	2549	23	42
+15717	1	chr19	25201136	7106	1	chr19	12502309	2776	42	42
+15886	1	chr19	49263587	14680	0	chr19	49277415	14688	42	42
+15918	0	chr19	17575582	4508	1	chr19	18115657	4694	42	42
+16042	0	chr19	25368746	7151	1	chr19	25399455	7161	42	42
+16510	1	chr19	39875617	11957	1	chr19	8221528	1397	32	42
+16798	0	chr19	24397063	6872	1	chr19	38784704	11614	24	42
+16936	1	chr19	23896603	6735	1	chr19	4090245	324	42	42
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Binary file test-data/output.cool has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample	Mon Oct 24 15:19:04 2022 +0000
@@ -0,0 +1,29 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files.  You will need
+#to create these data files and then create a fasta_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The fasta_indexes.loc
+#file has this format (white space characters are TAB characters):
+#
+# <unique_build_id>	<dbkey>	<display_name>	<file_base_path>
+#
+#So, for example, if you had hg19 Canonical indexed stored in
+#
+# /depot/data2/galaxy/hg19/sam/,
+#
+#then the fasta_indexes.loc entry would look like this:
+#
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#
+#and your /depot/data2/galaxy/hg19/sam/ directory
+#would contain hg19canon.fa and hg19canon.fa.fai files.
+#
+#Your fasta_indexes.loc file should include an entry per line for
+#each index set you have stored.  The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file.  For example:
+#
+#hg18canon	hg18	Human (Homo sapiens): hg18 Canonical	/depot/data2/galaxy/hg18/sam/hg18canon.fa
+#hg18full	hg18	Human (Homo sapiens): hg18 Full	/depot/data2/galaxy/hg18/sam/hg18full.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/depot/data2/galaxy/hg19/sam/hg19full.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Mon Oct 24 15:19:04 2022 +0000
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Location of SAMTools indexes for FASTA files -->
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/fasta_indexes.loc" />
+    </table>
+</tables>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Mon Oct 24 15:19:04 2022 +0000
@@ -0,0 +1,6 @@
+<tables>
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/fasta_indexes.loc" />
+    </table>
+</tables>
Binary file workflow_cooler.pdf has changed