| Previous changeset 1:44de678a44c4 (2018-10-15) Next changeset 3:56faa6a57e50 (2022-08-15) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit 0f75269223c0821c6c82acf98fde947d0f816f2b" |
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modified:
macros.xml samtools_depth.xml test-data/samtools_depth_out4.tab |
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added:
test-data/samtools_depth_out5.tab test-data/samtools_depth_out6.tab test-data/samtools_depth_out7.tab |
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| diff -r 44de678a44c4 -r 2ee8dc1aeda9 macros.xml --- a/macros.xml Mon Oct 15 10:10:39 2018 -0400 +++ b/macros.xml Tue Sep 28 16:12:22 2021 +0000 |
| [ |
| @@ -5,10 +5,16 @@ <yield/> </requirements> </xml> - <token name="@TOOL_VERSION@">1.9</token> - <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token> + <token name="@TOOL_VERSION@">1.13</token> + <token name="@PROFILE@">20.05</token> + <token name="@FLAGS@"><![CDATA[ + #set $flags = 0 + #if $filter + #set $flags = sum(map(int, str($filter).split(','))) + #end if + ]]></token> <token name="@PREPARE_IDX@"><![CDATA[ - ##prepare input and indices + ##prepare input and indices ln -s '$input' infile && #if $input.is_of_type('bam'): #if str( $input.metadata.bam_index ) != "None": @@ -25,7 +31,7 @@ #end if ]]></token> <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[ - ##prepare input and indices + ##prepare input and indices #for $i, $bam in enumerate( $input_bams ): ln -s '$bam' '${i}' && #if $bam.is_of_type('bam'): @@ -63,6 +69,51 @@ #set reffai=None #end if ]]></token> + + <xml name="optional_reference"> + <conditional name="addref_cond"> + <param name="addref_select" type="select" label="Use a reference sequence"> + <help>@HELP@</help> + <option value="no">No</option> + <option value="history">Use a genome/index from the history</option> + <option value="cached">Use a built-in genome</option> + </param> + <when value="no"/> + <when value="history"> + <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/> + </when> + <when value="cached"> + <param name="ref" argument="@ARGUMENT@" type="select" label="Reference"> + <options from_data_table="fasta_indexes"> + <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/> + </options> + <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset"/> + </param> + </when> + </conditional> + </xml> + <xml name="mandatory_reference" token_help="" token_argument=""> + <conditional name="addref_cond"> + <param name="addref_select" type="select" label="Use a reference sequence"> + <help>@HELP@</help> + <option value="history">Use a genome/index from the history</option> + <option value="cached">Use a built-in genome</option> + </param> + <when value="history"> + <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/> + </when> + <when value="cached"> + <param name="ref" argument="@ARGUMENT@" type="select" label="Reference"> + <options from_data_table="fasta_indexes"> + <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/> + <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" /> + </options> + </param> + </when> + </conditional> + </xml> + + <token name="@ADDTHREADS@"><![CDATA[ ##compute the number of ADDITIONAL threads to be used by samtools (-@) addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) && @@ -70,28 +121,28 @@ <token name="@ADDMEMORY@"><![CDATA[ ##compute the number of memory available to samtools sort (-m) ##use only 75% of available: https://github.com/samtools/samtools/issues/831 - addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && + addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ]]></token> <xml name="seed_input"> - <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." /> + <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." /> </xml> - <xml name="flag_options"> - <option value="1">read is paired</option> - <option value="2">read is mapped in a proper pair</option> - <option value="4">read is unmapped</option> - <option value="8">mate is unmapped</option> - <option value="16">read reverse strand</option> - <option value="32">mate reverse strand</option> - <option value="64">read is the first in a pair</option> - <option value="128">read is the second in a pair</option> - <option value="256">alignment or read is not primary</option> - <option value="512">read fails platform/vendor quality checks</option> - <option value="1024">read is a PCR or optical duplicate</option> - <option value="2048">supplementary alignment</option> + <xml name="flag_options" token_s1="false" token_s2="false" token_s4="false" token_s8="false" token_s16="false" token_s32="false" token_s64="false" token_s128="false" token_s256="false" token_s512="false" token_s1024="false" token_s2048="false"> + <option value="1" selected="@S1@">Read is paired</option> + <option value="2" selected="@S2@">Read is mapped in a proper pair</option> + <option value="4" selected="@S4@">Read is unmapped</option> + <option value="8" selected="@S8@">Mate is unmapped</option> + <option value="16" selected="@S16@">Read is mapped to the reverse strand of the reference</option> + <option value="32" selected="@S32@">Mate is mapped to the reverse strand of the reference</option> + <option value="64" selected="@S64@">Read is the first in a pair</option> + <option value="128" selected="@S128@">Read is the second in a pair</option> + <option value="256" selected="@S256@">Alignment of the read is not primary</option> + <option value="512" selected="@S512@">Read fails platform/vendor quality checks</option> + <option value="1024" selected="@S1024@">Read is a PCR or optical duplicate</option> + <option value="2048" selected="@S2048@">Alignment is supplementary</option> </xml> - <!-- region specification macros and tokens for tools that allow the specification + <!-- region specification macros and tokens for tools that allow the specification of region by bed file / space separated list of regions --> <token name="@REGIONS_FILE@"><![CDATA[ #if $cond_region.select_region == 'tab': |
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| diff -r 44de678a44c4 -r 2ee8dc1aeda9 samtools_depth.xml --- a/samtools_depth.xml Mon Oct 15 10:10:39 2018 -0400 +++ b/samtools_depth.xml Tue Sep 28 16:12:22 2021 +0000 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="samtools_depth" name="Samtools depth" version="@TOOL_VERSION@"> +<tool id="samtools_depth" name="Samtools depth" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>compute the depth at each position or region</description> <macros> <import>macros.xml</import> @@ -32,6 +32,15 @@ #for $i in range(len( $input_bams )): ${i} #end for +#set $filter = $additional_options.required_flags +@FLAGS@ +-g $flags +#set $filter = $additional_options.skipped_flags +@FLAGS@ +-G $flags +$additional_options.deletions +$additional_options.single_read +$output_options.header > '${output}' ]]></command> <inputs> @@ -61,11 +70,30 @@ <param name="basequality" type="integer" argument="-q" min="0" optional="true" label="Only count reads with base quality greater than" /> <param name="mapquality" type="integer" argument="-Q" min="0" optional="true" label="Only count reads with mapping quality greater than" /> + + <section name="additional_options" title="Additional Filter Options"> + <param name="required_flags" argument="-g" type="select" multiple="True" label="Require that these flags are set."> + <expand macro="flag_options" /> + </param> + + <param name="skipped_flags" argument="-G" type="select" multiple="True" label="Exclude reads with any of the following flags set (the default set is UNMAP,SECONDARY,QCFAIL,DUP or 0x704)."> + <expand macro="flag_options" s4="true" s256="true" s512="true" s1024="true"/> + </param> + + <param name="deletions" type="boolean" argument="-J" truevalue="-J" falsevalue="" checked="false" label="Include reads with deletions in depth computation." /> + <param name="single_read" type="boolean" argument="-s" truevalue="-s" falsevalue="" checked="false" label="For the overlapping section of a read pair, count only the bases of a single read." /> + </section> + + <section name="output_options" title="Output Options" expanded="true"> + <param name="header" type="boolean" argument="-H" truevalue="-H" falsevalue="" checked="false" label="Print a file header to file." /> + </section> + </inputs> <outputs> <data name="output" format="tabular" label="${tool.name} on ${on_string}" /> </outputs> <tests> + <!-- 1) --> <test> <conditional name="cond_region"> <param name="select_region" value="bed"/> @@ -74,6 +102,7 @@ <param name="input_bams" value="eboVir3.bam" ftype="bam" /> <output name="output" file="samtools_depth_out1.tab" /> </test> + <!-- 2) --> <test> <conditional name="cond_region"> <param name="select_region" value="text"/> @@ -82,11 +111,13 @@ <param name="input_bams" value="eboVir3.bam" ftype="bam" /> <output name="output" file="samtools_depth_out2.tab" /> </test> + <!-- 3) --> <test> <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" /> <param name="all" value="-a"/> <output name="output" file="samtools_depth_out3.tab" /> </test> + <!-- 4) --> <test> <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" /> <param name="minlength" value="10" /> @@ -97,6 +128,28 @@ <param name="mapquality" value="12" /> <output name="output" file="samtools_depth_out4.tab" /> </test> + <!-- 5) Testing argument -H --> + <test> + <conditional name="cond_region"> + <param name="select_region" value="bed"/> + <param name="input_bed" value="eboVir3.1.bed" ftype="bed" /> + </conditional> + <param name="input_bams" value="eboVir3.bam" ftype="bam" /> + <param name="header" value="true" /> + <output name="output" file="samtools_depth_out5.tab" /> + </test> + <!-- 6) Tetsing argument -g --> + <test> + <param name="input_bams" value="eboVir3.bam" ftype="bam" /> + <param name="required_flags" value="2,16,64" /> + <output name="output" file="samtools_depth_out6.tab" /> + </test> + <!-- 7) Tetsing argument -G --> + <test> + <param name="input_bams" value="eboVir3.bam" ftype="bam" /> + <param name="skipped_flags" value="2,16,64" /> + <output name="output" file="samtools_depth_out7.tab" /> + </test> </tests> <help> **What it does** |
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| diff -r 44de678a44c4 -r 2ee8dc1aeda9 test-data/samtools_depth_out4.tab --- a/test-data/samtools_depth_out4.tab Mon Oct 15 10:10:39 2018 -0400 +++ b/test-data/samtools_depth_out4.tab Tue Sep 28 16:12:22 2021 +0000 |
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| b'@@ -481,76 +481,76 @@\n eboVir3\t491\t3\t0\n eboVir3\t492\t3\t0\n eboVir3\t493\t3\t0\n-eboVir3\t494\t4\t0\n-eboVir3\t495\t4\t0\n-eboVir3\t496\t4\t0\n-eboVir3\t497\t4\t0\n-eboVir3\t498\t4\t0\n-eboVir3\t499\t4\t0\n-eboVir3\t500\t4\t0\n-eboVir3\t501\t4\t0\n-eboVir3\t502\t5\t0\n-eboVir3\t503\t5\t0\n-eboVir3\t504\t5\t0\n-eboVir3\t505\t5\t0\n-eboVir3\t506\t5\t0\n-eboVir3\t507\t5\t0\n-eboVir3\t508\t5\t0\n-eboVir3\t509\t5\t0\n-eboVir3\t510\t6\t0\n-eboVir3\t511\t6\t0\n-eboVir3\t512\t6\t0\n-eboVir3\t513\t6\t0\n-eboVir3\t514\t6\t0\n-eboVir3\t515\t6\t0\n-eboVir3\t516\t6\t0\n-eboVir3\t517\t6\t0\n-eboVir3\t518\t6\t0\n-eboVir3\t519\t6\t0\n-eboVir3\t520\t6\t0\n-eboVir3\t521\t6\t0\n-eboVir3\t522\t6\t0\n-eboVir3\t523\t6\t0\n-eboVir3\t524\t6\t0\n-eboVir3\t525\t6\t0\n-eboVir3\t526\t5\t0\n-eboVir3\t527\t6\t0\n-eboVir3\t528\t5\t0\n-eboVir3\t529\t6\t0\n-eboVir3\t530\t6\t0\n-eboVir3\t531\t6\t0\n-eboVir3\t532\t6\t0\n-eboVir3\t533\t6\t0\n-eboVir3\t534\t6\t0\n-eboVir3\t535\t6\t0\n-eboVir3\t536\t6\t0\n-eboVir3\t537\t6\t0\n-eboVir3\t538\t7\t0\n-eboVir3\t539\t7\t0\n-eboVir3\t540\t7\t0\n-eboVir3\t541\t7\t0\n-eboVir3\t542\t7\t0\n-eboVir3\t543\t7\t0\n-eboVir3\t544\t7\t0\n-eboVir3\t545\t7\t0\n-eboVir3\t546\t7\t0\n-eboVir3\t547\t7\t0\n-eboVir3\t548\t7\t0\n-eboVir3\t549\t7\t0\n-eboVir3\t550\t7\t0\n-eboVir3\t551\t7\t0\n-eboVir3\t552\t8\t0\n-eboVir3\t553\t8\t0\n-eboVir3\t554\t8\t0\n-eboVir3\t555\t7\t0\n-eboVir3\t556\t7\t0\n-eboVir3\t557\t7\t0\n-eboVir3\t558\t7\t0\n-eboVir3\t559\t7\t0\n-eboVir3\t560\t7\t0\n-eboVir3\t561\t7\t0\n-eboVir3\t562\t7\t0\n-eboVir3\t563\t7\t0\n+eboVir3\t494\t5\t0\n+eboVir3\t495\t5\t0\n+eboVir3\t496\t5\t0\n+eboVir3\t497\t5\t0\n+eboVir3\t498\t5\t0\n+eboVir3\t499\t5\t0\n+eboVir3\t500\t5\t0\n+eboVir3\t501\t5\t0\n+eboVir3\t502\t6\t0\n+eboVir3\t503\t6\t0\n+eboVir3\t504\t6\t0\n+eboVir3\t505\t6\t0\n+eboVir3\t506\t6\t0\n+eboVir3\t507\t6\t0\n+eboVir3\t508\t6\t0\n+eboVir3\t509\t6\t0\n+eboVir3\t510\t7\t0\n+eboVir3\t511\t7\t0\n+eboVir3\t512\t7\t0\n+eboVir3\t513\t7\t0\n+eboVir3\t514\t7\t0\n+eboVir3\t515\t7\t0\n+eboVir3\t516\t7\t0\n+eboVir3\t517\t7\t0\n+eboVir3\t518\t7\t0\n+eboVir3\t519\t7\t0\n+eboVir3\t520\t7\t0\n+eboVir3\t521\t7\t0\n+eboVir3\t522\t7\t0\n+eboVir3\t523\t7\t0\n+eboVir3\t524\t7\t0\n+eboVir3\t525\t7\t0\n+eboVir3\t526\t6\t0\n+eboVir3\t527\t7\t0\n+eboVir3\t528\t6\t0\n+eboVir3\t529\t7\t0\n+eboVir3\t530\t7\t0\n+eboVir3\t531\t7\t0\n+eboVir3\t532\t7\t0\n+eboVir3\t533\t7\t0\n+eboVir3\t534\t7\t0\n+eboVir3\t535\t7\t0\n+eboVir3\t536\t7\t0\n+eboVir3\t537\t7\t0\n+eboVir3\t538\t8\t0\n+eboVir3\t539\t8\t0\n+eboVir3\t540\t8\t0\n+eboVir3\t541\t8\t0\n+eboVir3\t542\t8\t0\n+eboVir3\t543\t8\t0\n+eboVir3\t544\t8\t0\n+eboVir3\t545\t8\t0\n+eboVir3\t546\t8\t0\n+eboVir3\t547\t8\t0\n+eboVir3\t548\t8\t0\n+eboVir3\t549\t8\t0\n+eboVir3\t550\t8\t0\n+eboVir3\t551\t8\t0\n+eboVir3\t552\t9\t0\n+eboVir3\t553\t9\t0\n+eboVir3\t554\t9\t0\n+eboVir3\t555\t8\t0\n+eboVir3\t556\t8\t0\n+eboVir3\t557\t8\t0\n+eboVir3\t558\t8\t0\n+eboVir3\t559\t8\t0\n+eboVir3\t560\t8\t0\n+eboVir3\t561\t8\t0\n+eboVir3\t562\t8\t0\n+eboVir3\t563\t8\t0\n eboVir3\t564\t6\t0\n eboVir3\t565\t6\t0\n eboVir3\t566\t6\t0\n@@ -581,76 +581,76 @@\n eboVir3\t591\t9\t0\n eboVir3\t592\t10\t0\n eboVir3\t593\t10\t0\n-eboVir3\t594\t11\t0\n-eboVir3\t595\t11\t0\n-eboVir3\t596\t11\t0\n-eboVir3\t597\t10\t0\n-eboVir3\t598\t11\t0\n-eboVir3\t599\t10\t0\n-eboVir3\t600\t10\t0\n-eboVir3\t601\t10\t0\n-eboVir3\t602\t10\t0\n-eboVir3\t603\t10\t0\n-eboVir3\t604\t10\t0\n-eboVir3\t605\t10\t0\n-eboVir3\t606\t10\t0\n-eboVir3\t607\t10\t0\n-eboVir3\t608\t9\t0\n-eboVir3\t609\t9\t0\n-eboVir3\t610\t9\t0\n-eboVir3\t611\t9\t0\n-eboVir3\t612\t9\t0\n-eboVir3\t613\t9\t0\n-eboVir3\t614\t9\t0\n-eboVir3\t615\t9\t0\n-eboVir3\t616\t9\t0\n-eboVir3\t617\t9\t0\n-eboVir3\t618\t9\t0\n-eboVir3\t619\t9\t0\n-eboVir3\t620\t9\t0\n-eboVir3\t621\t10\t0\n-eboVir3\t622\t9\t0\n-eboVir3\t623\t9\t0\n-eboVir3\t624\t9\t0\n-eboVir3\t625\t9\t0\n-eboVir3\t626\t9\t0\n-eboVir3\t627\t9\t0\n-eboVir3\t628\t10\t0\n-eboVir3\t629\t11\t0\n-eboVir3\t630\t11\t0\n-eboVir3\t631\t11\t0\n-eboVir3\t632\t11\t0\n-eboVir3\t633\t11\t0\n-eboVir3\t634\t11\t0\n-eboVir3\t635\t11\t0\n-eboVir3\t636\t11\t0\n-eboVir3\t637\t11\t0\n-eboVir3\t638\t11\t0\n-eboVir3\t639\t11\t0\n-eboVir3\t640\t11\t0\n-eboVir3\t641\t10\t0\n-eboVir3\t642\t10\t0\n-eboVir3\t643\t10\t0\n-eboVir3\t644\t10\t0\n-eboVir3\t645\t9\t0\n-eboVir3\t646\t9\t0\n-eboVir3\t647\t10\t0\n-eboVir3\t648\t9\t0\n-eboVir3\t649\t9\t0\n-eboVir3\t650\t8\t0\n-eboVir3\t651\t8\t0\n-eboVir3\t652\t7\t0\n-eboVir3\t653\t7\t0\n-eboVir3\t654\t7\t0\n-eboVir3\t655\t7\t0\n-eboVir3\t656\t7\t0\n-eboVir3\t657\t7\t0\n-eboVir3\t658\t8\t0\n-eboVir3\t659\t8\t0\n-eboVir3\t660\t8\t0\n-eboVir3\t661\t8\t0\n-eboVir3\t662\t7\t0\n-eboVir3\t663\t7\t0\n+eboVir3\t594\t12\t0\n+eboVir3\t595\t12\t0\n+eboVir3\t596\t12\t0\n+eboVir3\t597\t11\t0\n+eboVir3\t598\t12\t0\n+eboVir3\t599\t11\t0\n+eboVir3\t600\t11\t0\n+eboVir3\t601\t11\t0\n+eboVir3\t602\t11\t0\n+eboVir3\t603\t11\t0\n+eboVir3\t604\t11\t0'..b'r3\t18252\t9\t0\n+eboVir3\t18253\t9\t0\n+eboVir3\t18254\t9\t0\n+eboVir3\t18255\t10\t0\n+eboVir3\t18256\t10\t0\n+eboVir3\t18257\t10\t0\n+eboVir3\t18258\t11\t0\n+eboVir3\t18259\t11\t0\n+eboVir3\t18260\t11\t0\n+eboVir3\t18261\t11\t0\n+eboVir3\t18262\t11\t0\n+eboVir3\t18263\t10\t0\n+eboVir3\t18264\t10\t0\n+eboVir3\t18265\t10\t0\n+eboVir3\t18266\t10\t0\n+eboVir3\t18267\t10\t0\n+eboVir3\t18268\t10\t0\n+eboVir3\t18269\t10\t0\n+eboVir3\t18270\t11\t0\n+eboVir3\t18271\t11\t0\n+eboVir3\t18272\t11\t0\n+eboVir3\t18273\t11\t0\n+eboVir3\t18274\t11\t0\n+eboVir3\t18275\t11\t0\n+eboVir3\t18276\t11\t0\n+eboVir3\t18277\t10\t0\n+eboVir3\t18278\t10\t0\n+eboVir3\t18279\t10\t0\n+eboVir3\t18280\t10\t0\n+eboVir3\t18281\t10\t0\n+eboVir3\t18282\t10\t0\n+eboVir3\t18283\t10\t0\n+eboVir3\t18284\t9\t0\n+eboVir3\t18285\t9\t0\n+eboVir3\t18286\t9\t0\n+eboVir3\t18287\t9\t0\n+eboVir3\t18288\t8\t0\n+eboVir3\t18289\t8\t0\n+eboVir3\t18290\t8\t0\n+eboVir3\t18291\t8\t0\n+eboVir3\t18292\t8\t0\n+eboVir3\t18293\t8\t0\n+eboVir3\t18294\t8\t0\n+eboVir3\t18295\t9\t0\n+eboVir3\t18296\t9\t0\n+eboVir3\t18297\t8\t0\n+eboVir3\t18298\t8\t0\n+eboVir3\t18299\t8\t0\n+eboVir3\t18300\t9\t0\n+eboVir3\t18301\t9\t0\n+eboVir3\t18302\t9\t0\n+eboVir3\t18303\t10\t0\n+eboVir3\t18304\t10\t0\n+eboVir3\t18305\t10\t0\n+eboVir3\t18306\t10\t0\n+eboVir3\t18307\t10\t0\n+eboVir3\t18308\t10\t0\n+eboVir3\t18309\t9\t0\n eboVir3\t18310\t7\t0\n eboVir3\t18311\t7\t0\n eboVir3\t18312\t7\t0\n@@ -18455,76 +18455,76 @@\n eboVir3\t18465\t5\t0\n eboVir3\t18466\t5\t0\n eboVir3\t18467\t5\t0\n-eboVir3\t18468\t6\t0\n-eboVir3\t18469\t6\t0\n-eboVir3\t18470\t6\t0\n-eboVir3\t18471\t7\t0\n-eboVir3\t18472\t7\t0\n-eboVir3\t18473\t7\t0\n-eboVir3\t18474\t7\t0\n-eboVir3\t18475\t7\t0\n-eboVir3\t18476\t7\t0\n-eboVir3\t18477\t8\t0\n-eboVir3\t18478\t8\t0\n-eboVir3\t18479\t8\t0\n-eboVir3\t18480\t8\t0\n-eboVir3\t18481\t8\t0\n-eboVir3\t18482\t8\t0\n-eboVir3\t18483\t8\t0\n-eboVir3\t18484\t8\t0\n-eboVir3\t18485\t9\t0\n-eboVir3\t18486\t9\t0\n-eboVir3\t18487\t9\t0\n-eboVir3\t18488\t9\t0\n-eboVir3\t18489\t9\t0\n-eboVir3\t18490\t9\t0\n-eboVir3\t18491\t9\t0\n-eboVir3\t18492\t9\t0\n-eboVir3\t18493\t9\t0\n-eboVir3\t18494\t9\t0\n-eboVir3\t18495\t9\t0\n-eboVir3\t18496\t8\t0\n-eboVir3\t18497\t8\t0\n-eboVir3\t18498\t7\t0\n-eboVir3\t18499\t7\t0\n-eboVir3\t18500\t7\t0\n-eboVir3\t18501\t7\t0\n-eboVir3\t18502\t7\t0\n-eboVir3\t18503\t7\t0\n-eboVir3\t18504\t7\t0\n-eboVir3\t18505\t7\t0\n-eboVir3\t18506\t6\t0\n-eboVir3\t18507\t6\t0\n-eboVir3\t18508\t6\t0\n-eboVir3\t18509\t7\t0\n-eboVir3\t18510\t7\t0\n-eboVir3\t18511\t7\t0\n-eboVir3\t18512\t7\t0\n-eboVir3\t18513\t7\t0\n-eboVir3\t18514\t7\t0\n-eboVir3\t18515\t7\t0\n-eboVir3\t18516\t7\t0\n-eboVir3\t18517\t7\t0\n-eboVir3\t18518\t7\t0\n-eboVir3\t18519\t7\t0\n-eboVir3\t18520\t8\t0\n-eboVir3\t18521\t8\t0\n-eboVir3\t18522\t8\t0\n-eboVir3\t18523\t8\t0\n-eboVir3\t18524\t8\t0\n-eboVir3\t18525\t8\t0\n-eboVir3\t18526\t7\t0\n-eboVir3\t18527\t7\t0\n-eboVir3\t18528\t6\t0\n-eboVir3\t18529\t6\t0\n-eboVir3\t18530\t6\t0\n-eboVir3\t18531\t6\t0\n-eboVir3\t18532\t6\t0\n-eboVir3\t18533\t6\t0\n-eboVir3\t18534\t6\t0\n-eboVir3\t18535\t6\t0\n-eboVir3\t18536\t6\t0\n-eboVir3\t18537\t6\t0\n+eboVir3\t18468\t7\t0\n+eboVir3\t18469\t7\t0\n+eboVir3\t18470\t7\t0\n+eboVir3\t18471\t8\t0\n+eboVir3\t18472\t8\t0\n+eboVir3\t18473\t8\t0\n+eboVir3\t18474\t8\t0\n+eboVir3\t18475\t8\t0\n+eboVir3\t18476\t8\t0\n+eboVir3\t18477\t9\t0\n+eboVir3\t18478\t9\t0\n+eboVir3\t18479\t9\t0\n+eboVir3\t18480\t9\t0\n+eboVir3\t18481\t9\t0\n+eboVir3\t18482\t9\t0\n+eboVir3\t18483\t9\t0\n+eboVir3\t18484\t9\t0\n+eboVir3\t18485\t10\t0\n+eboVir3\t18486\t10\t0\n+eboVir3\t18487\t10\t0\n+eboVir3\t18488\t10\t0\n+eboVir3\t18489\t10\t0\n+eboVir3\t18490\t10\t0\n+eboVir3\t18491\t10\t0\n+eboVir3\t18492\t10\t0\n+eboVir3\t18493\t10\t0\n+eboVir3\t18494\t10\t0\n+eboVir3\t18495\t10\t0\n+eboVir3\t18496\t9\t0\n+eboVir3\t18497\t9\t0\n+eboVir3\t18498\t8\t0\n+eboVir3\t18499\t8\t0\n+eboVir3\t18500\t8\t0\n+eboVir3\t18501\t8\t0\n+eboVir3\t18502\t8\t0\n+eboVir3\t18503\t8\t0\n+eboVir3\t18504\t8\t0\n+eboVir3\t18505\t8\t0\n+eboVir3\t18506\t7\t0\n+eboVir3\t18507\t7\t0\n+eboVir3\t18508\t7\t0\n+eboVir3\t18509\t8\t0\n+eboVir3\t18510\t8\t0\n+eboVir3\t18511\t8\t0\n+eboVir3\t18512\t8\t0\n+eboVir3\t18513\t8\t0\n+eboVir3\t18514\t8\t0\n+eboVir3\t18515\t8\t0\n+eboVir3\t18516\t8\t0\n+eboVir3\t18517\t8\t0\n+eboVir3\t18518\t8\t0\n+eboVir3\t18519\t8\t0\n+eboVir3\t18520\t9\t0\n+eboVir3\t18521\t9\t0\n+eboVir3\t18522\t9\t0\n+eboVir3\t18523\t9\t0\n+eboVir3\t18524\t9\t0\n+eboVir3\t18525\t9\t0\n+eboVir3\t18526\t8\t0\n+eboVir3\t18527\t8\t0\n+eboVir3\t18528\t7\t0\n+eboVir3\t18529\t7\t0\n+eboVir3\t18530\t7\t0\n+eboVir3\t18531\t7\t0\n+eboVir3\t18532\t7\t0\n+eboVir3\t18533\t7\t0\n+eboVir3\t18534\t7\t0\n+eboVir3\t18535\t7\t0\n+eboVir3\t18536\t7\t0\n+eboVir3\t18537\t7\t0\n eboVir3\t18538\t5\t0\n eboVir3\t18539\t5\t0\n eboVir3\t18540\t5\t0\n' |
| b |
| diff -r 44de678a44c4 -r 2ee8dc1aeda9 test-data/samtools_depth_out5.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_depth_out5.tab Tue Sep 28 16:12:22 2021 +0000 |
| b |
| b'@@ -0,0 +1,2501 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|
| b |
| diff -r 44de678a44c4 -r 2ee8dc1aeda9 test-data/samtools_depth_out6.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_depth_out6.tab Tue Sep 28 16:12:22 2021 +0000 |
| b |
| b'@@ -0,0 +1,18945 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|
| b |
| diff -r 44de678a44c4 -r 2ee8dc1aeda9 test-data/samtools_depth_out7.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_depth_out7.tab Tue Sep 28 16:12:22 2021 +0000 |
| b |
| b'@@ -0,0 +1,15545 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