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Changeset 15:c44f824c051a (2024-02-08)

Previous changeset 14:3ff17bad4006 (2023-08-28)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus commit 8fc43fe1e8c12438a14dbd174a8af3e7cb8b55dc

modified:
cactus_export.xml
macros.xml

removed:
test-data/evolverMammals.hal
test-data/evolverMammals.maf
test-data/evolverMammals_both.maf
test-data/evolverMammals_noroot.hal
test-data/evolverMammals_noroot.maf
test-data/germ_25.fasta.gz
test-data/hal2maf.maf
test-data/pens_25.fasta.gz
test-data/set_reference.maf
test-data/vulg_25.fasta.gz
test-data/within.hal

diff -r 3ff17bad4006 -r c44f824c051a cactus_export.xml
--- a/cactus_export.xml Mon Aug 28 23:09:49 2023 +0000
+++ b/cactus_export.xml Thu Feb 08 08:52:41 2024 +0000

[

@@ -6,13 +6,12 @@
     <expand macro="xrefs"/>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
-        export TMPDIR=\${_GALAXY_JOB_TMP_DIR} &&

         ## check if the reference level was specified
         #if $export_select.format in ['maf_selector', 'vg_selector']:
             #if $export_select.ref_level == '':
                 echo "You must provide a reference level" &&
-                exit 1
+                exit 1 ;
             #end if
         #end if

@@ -32,7 +31,7 @@
             &&
             hal2assemblyHub.py
             --maxCores  \${GALAXY_SLOTS:-4}
-            --maxMemory \${GALAXY_MEMORY_MB:-8192}M
+            --maxMemory \${GALAXY_MEMORY_MB:-8196}M
             ./jobStore
             alignment.hal
             assemblyhub
@@ -50,7 +49,7 @@

     ]]></command>
     <inputs>
-        <param name="hal_file" type="data" format="h5" label="HAL file" help="Multiple-genome alignment generated by Cactus" />
+        <param name="hal_file" type="data" format="h5" label="HAL file" help="Multiple-genome alignment generated by Cactus"/>
         <conditional name="export_select">
             <param name="format" type="select" label="Output format" help="The type of output you want to export. Run this tool once for each output format.">
                 <option value="maf_selector" selected="true">MAF file</option>
@@ -58,23 +57,23 @@
                 <option value="vg_selector">VG file</option>
             </param>
             <when value="maf_selector">
-                <param name="ref_level" type="text" value="" label="Reference genome" help="Specify one of the Input Genomes as the reference level. This must match the label used in 'Genome Label'." />
+                <param name="ref_level" type="text" value="" label="Reference genome" help="Specify one of the Input Genomes as the reference level. This must match the label used in 'Genome Label'."/>
             </when>
             <when value="ah_selector">
             </when>
             <when value="vg_selector">
-                <param name="ref_level" type="text" value="" label="Reference genome" help="Specify one of the Input Genomes as the reference level. This must match the label used in 'Genome Label'." />
+                <param name="ref_level" type="text" value="" label="Reference genome" help="Specify one of the Input Genomes as the reference level. This must match the label used in 'Genome Label'."/>
             </when>
         </conditional>
     </inputs>
     <outputs>
-        <data name="out_maf" format="maf" from_work_dir="alignment.maf" label="${tool.name} on ${on_string} (MAF file)" >
+        <data name="out_maf" format="maf" from_work_dir="alignment.maf" label="${tool.name} on ${on_string} (MAF file)">
             <filter>export_select['format'] == 'maf_selector'</filter>
         </data>
-        <data name="out_vg" format="vg" from_work_dir="alignment.pg" label="${tool.name} on ${on_string} (VG file)" >
+        <data name="out_vg" format="vg" from_work_dir="alignment.pg" label="${tool.name} on ${on_string} (VG file)">
             <filter>export_select['format'] == 'vg_selector'</filter>
         </data>
-        <data name="out_ah" format="tar" from_work_dir="assemblyhub.tar" label="${tool.name} on ${on_string} (Assembly Hub)" >
+        <data name="out_ah" format="tar" from_work_dir="assemblyhub.tar" label="${tool.name} on ${on_string} (Assembly Hub)">
             <filter>export_select['format'] == 'ah_selector'</filter>
         </data>
     </outputs>
@@ -82,34 +81,34 @@
         
         <test expect_failure="true">
             <conditional name="export_select">
-                <param name="format" value="maf_selector" />
+                <param name="format" value="maf_selector"/>
             </conditional>
-            <param name="hal_file" ftype="h5" value="evolverMammals.hal" />
+            <param name="hal_file" ftype="h5" location="https://zenodo.org/record/8336793/files/evolverMammals.hal"/>
         </test>
         
         <test expect_num_outputs="1">
             <conditional name="export_select">
-                <param name="ref_level" value="simMouse_chr6" />
-                <param name="format" value="maf_selector" />
+                <param name="ref_level" value="simMouse_chr6"/>
+                <param name="format" value="maf_selector"/>
             </conditional>
-            <param name="hal_file" ftype="h5" value="within.hal" />
-            <output name="out_maf" file="set_reference.maf" />
+            <param name="hal_file" ftype="h5" location="https://zenodo.org/record/8336793/files/within.hal"/>
+            <output name="out_maf" location="https://zenodo.org/record/8336793/files/set_reference.maf"/>
         </test>
         
         <test expect_num_outputs="1">
             <conditional name="export_select">
-                <param name="ref_level" value="simMouse_chr6" />
-                <param name="format" value="maf_selector" />
+                <param name="ref_level" value="simMouse_chr6"/>
+                <param name="format" value="maf_selector"/>
             </conditional>
-            <param name="hal_file" ftype="h5" value="evolverMammals_noroot.hal" />
-            <output name="out_maf" file="evolverMammals_noroot.maf" />
+            <param name="hal_file" ftype="h5" location="https://zenodo.org/record/8336793/files/evolverMammals_noroot.hal"/>
+            <output name="out_maf" location="https://zenodo.org/record/8336793/files/evolverMammals_noroot.maf"/>
         </test>
         
         <test expect_num_outputs="1">
             <conditional name="export_select">
-                <param name="format" value="ah_selector" />
+                <param name="format" value="ah_selector"/>
             </conditional>
-            <param name="hal_file" ftype="h5" value="within.hal" />
+            <param name="hal_file" ftype="h5" location="https://zenodo.org/record/8336793/files/within.hal"/>
             <output name="out_ah">
                 <assert_contents>
                     <has_archive_member path="assemblyhub/hub.txt"/>
@@ -119,13 +118,13 @@
         
         <test expect_num_outputs="1">
             <conditional name="export_select">
-                <param name="format" value="vg_selector" />
-                <param name="ref_level" value="simMouse_chr6" />
+                <param name="format" value="vg_selector"/>
+                <param name="ref_level" value="simMouse_chr6"/>
             </conditional>
-            <param name="hal_file" ftype="h5" value="within.hal" />
+            <param name="hal_file" ftype="h5" location="https://zenodo.org/record/8336793/files/within.hal"/>
             <output name="out_vg">
                 <assert_contents>
-                        <has_size value="860452" delta="200000" />
+                    <has_size value="860452" delta="200000"/>
                 </assert_contents>
             </output>
         </test>

diff -r 3ff17bad4006 -r c44f824c051a macros.xml
--- a/macros.xml Mon Aug 28 23:09:49 2023 +0000
+++ b/macros.xml Thu Feb 08 08:52:41 2024 +0000

@@ -1,5 +1,5 @@
<macros>
-    <token name="@TOOL_VERSION@">2.6.7</token>
+    <token name="@TOOL_VERSION@">2.7.1</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">20.09</token>
     <xml name="requirements">

diff -r 3ff17bad4006 -r c44f824c051a test-data/evolverMammals.hal

Binary file test-data/evolverMammals.hal has changed

diff -r 3ff17bad4006 -r c44f824c051a test-data/evolverMammals.maf
--- a/test-data/evolverMammals.maf Mon Aug 28 23:09:49 2023 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,238809 +0,0 @@\n-##maf version=1 scoring=N/A\n-# hal ((simHuman_chr6:0.144018,(simMouse_chr6:0.084509,simRat_chr6:0.091589)mr:0.271974)Anc1:0.020593,(simCow_chr6:0.18908,simDog_chr6:0.16303)Anc2:0.032898)Anc0;\n-\n-a\n-s\tsimMouse_chr6.simMouse.chr6\t0\t4\t+\t636262\tTTTT\n-s\tAnc0.Anc0refChr9\t0\t4\t-\t35212\tTCTT\n-s\tAnc1.Anc1refChr0\t0\t4\t+\t16026\tTCTT\n-s\tAnc2.Anc2refChr0\t0\t4\t+\t56053\tTCTT\n-s\tmr.mrrefChr0\t0\t4\t+\t130230\tTTTT\n-s\tsimCow_chr6.simCow.chr6\t0\t4\t+\t602619\tTCTT\n-s\tsimDog_chr6.simDog.chr6\t0\t4\t+\t593897\tTCTT\n-s\tsimHuman_chr6.simHuman.chr6\t0\t4\t+\t601863\tTCTT\n-s\tsimRat_chr6.simRat.chr6\t0\t4\t+\t647215\tTTTT\n-\n-a\n-s\tsimMouse_chr6.simMouse.chr6\t4\t33\t+\t636262\tTCAGTTGCAATACCCAACCGGGAGAAACTTTCA\n-s\tAnc0.Anc0refChr9\t4\t33\t-\t35212\tTCTGGTGCAATACCCAATCTGTAGACAGTTTCA\n-s\tAnc1.Anc1refChr0\t4\t33\t+\t16026\tTCTGGTGCAATACCCAATCTGTAGACAGTTTCA\n-s\tAnc2.Anc2refChr0\t4\t33\t+\t56053\tTCTGGTGCACTACCCAATCTGTAGACAGTCTCA\n-s\tmr.mrrefChr0\t5\t33\t+\t130230\tTCAGTTGCAATACCCAACCTGGAGACACTTTCA\n-s\tsimCow_chr6.simCow.chr6\t4\t33\t+\t602619\tTCTGGTGCGCGACCCAATCTGTAGACGGACTTA\n-s\tsimDog_chr6.simDog.chr6\t5\t33\t+\t593897\tTCTGGTGCACTACCCAATCTGTAGACAGTCTCA\n-s\tsimHuman_chr6.simHuman.chr6\t4\t33\t+\t601863\tTCTGGTGCAATAGCCAATCTGCAAACAGTTTCA\n-s\tsimRat_chr6.simRat.chr6\t5\t31\t+\t647215\t--GGCTGCAATACCCAACCTGAAGACATTTTCA\n-\n-a\n-s\tsimMouse_chr6.simMouse.chr6\t37\t60\t+\t636262\tGTGAGCACACCTCAGGTTCCTATATCAAGCAGGCAGTCTTGCATAGCAAATGGTCTCTGG\n-s\tAnc0.Anc0refChr9\t39\t43\t-\t35212\tATGAGCACACCTTATGTGACTATATCAAGCA-----------------CATAGTCTTGCA\n-s\tAnc1.Anc1refChr0\t39\t60\t+\t16026\tATGAGCACACCTTATGTGACTATATCAAGCATACAGTCTTGCCTAGCACATAGTCTTGCA\n-s\tAnc2.Anc2refChr0\t39\t43\t+\t56053\tATGAGCACACCTTATGTGACTATATCAAGCA-----------------CATAGTCTTGCA\n-s\tmr.mrrefChr0\t38\t60\t+\t130230\tGTGAGCACACCTCAGGTTCCTATATCAAGCAGACAGTCTTGCATAGCAAATGGTCTCTGA\n-s\tsimCow_chr6.simCow.chr6\t39\t43\t+\t602619\tCTGAGCACACCTTATGTGATTATATCAAGCA-----------------GATAGTCTTGCA\n-s\tsimDog_chr6.simDog.chr6\t40\t41\t+\t593897\tAT--ACAAACCTTATGTGACTATATCAAGCA-----------------CATGGTCTTGCA\n-s\tsimHuman_chr6.simHuman.chr6\t39\t58\t+\t601863\tATGAGCACACCTTATATGAC--TATCAAGCATACAGTCTTGCCTAGCACACAATCTTGCA\n-s\tsimRat_chr6.simRat.chr6\t36\t60\t+\t647215\tGTGGGCCCACCTCAGGTTCTTATATCAAGCAGACAGTCTTGCGCAACAGATGGTCTCTGA\n-\n-a\n-s\tsimMouse_chr6.simMouse.chr6\t97\t41\t+\t636262\tTAGACGGTGCACTCAATCTATGTGAGGTATAGAAAATAAAG\n-s\tAnc0.Anc0refChr9\t82\t41\t-\t35212\tTAGATTGTGCAATCACTCTATCTGAGAGTCAGAGACCAAAG\n-s\tAnc1.Anc1refChr0\t99\t41\t+\t16026\tTAGATTGTGCAATCACTCTATCTGAGAGTCAGAGACCAAAG\n-s\tAnc2.Anc2refChr0\t82\t41\t+\t56053\tTAGATTGTGCAATGACTCTATCCAAGAGTCAGAGACCAGAG\n-s\tmr.mrrefChr0\t98\t41\t+\t130230\tTAGACGGTGCACTCAATCTATGTGAGGGATAGAAAACAAAG\n-s\tsimCow_chr6.simCow.chr6\t82\t41\t+\t602619\tTTGATTGTGCAATGACTCTATCCAAGAGTCAAAGACCAGAG\n-s\tsimDog_chr6.simDog.chr6\t81\t41\t+\t593897\tTAGATTGTGCAATGACTCTATCCAAGAGTCAGAGGCTGGAG\n-s\tsimHuman_chr6.simHuman.chr6\t98\t41\t+\t601863\tTAGATTGTACAATCTCTCGTTCTGGGAGTCAGAGACCAAAG\n-s\tsimRat_chr6.simRat.chr6\t96\t41\t+\t647215\tTAGACAGTGCACTCAATCTATGTGAAGGATAGAAAACAAAG\n-\n-a\n-s\tsimMouse_chr6.simMouse.chr6\t138\t39\t+\t636262\tGACTACACACATCTCATCAAGTATCCCGTCATATTTGTG\n-s\tAnc0.Anc0refChr9\t127\t37\t-\t35212\tTACT--GCATAGTTCATCGAGTATCCTGGAGTCTTGGTC\n-s\tAnc1.Anc1refChr0\t144\t37\t+\t16026\tTACT--GCATAGTTCATCGAGTATCCTGGAGTCTTGGTC\n-s\tAnc2.Anc2refChr0\t127\t37\t+\t56053\tTACT--GCATAGTTCATTGAGAATCCTGGAGTCTTGGTC\n-s\tmr.mrrefChr0\t139\t37\t+\t130230\tGACT--ACACATCTCATCAAGTATCCTGTCGTATTTGTG\n-s\tsimCow_chr6.simCow.chr6\t126\t36\t+\t602619\tTACG--GCATAGTTTATTG-GAATCCTGGAGTATGGGTC\n-s\tsimDog_chr6.simDog.chr6\t126\t37\t+\t593897\tTATT--ACATAGTTCTCTGAGAATCCTGGAGTCTTTATC\n-s\tsimHuman_chr6.simHuman.chr6\t143\t37\t+\t601863\tTACT--GTGTGGTTGATCGGGTATCCTGGAGTGTTGGTA\n-s\tsimRat_chr6.simRat.chr6\t137\t37\t+\t647215\tGACT--ACTCATCTCATCAAGTATCCTGTCGTATTTGTG\n-\n-a\n-s\tsimMouse_chr6.simMouse.chr6\t177\t9\t+\t636262\tGCAAAACAC\n-s\tAnc0.Anc0refChr9\t175\t9\t-\t35212\tGCAAAGCGC\n-s\tAnc1.Anc1refChr0\t192\t9\t+\t16026\tGCAAAGCGC\n-s\tAnc2.Anc2refChr0\t175\t9\t+\t56053\tGCAAAGCGC\n-s\tmr.mrrefChr0\t187\t9\t+\t130230\tGCAAAACAC\n-s\tsimCow_chr6.simCow.chr6\t173\t9\t+\t602619\tGCAAAGCAC\n-s\tsimDog_chr6.simDog.chr6\t174\t9\t+\t593897\tGCAAAGCGC\n-s\tsimHuman_chr6.simHuman.chr6\t191\t4\t+\t601863\tA'..b'r6\t593734\t7\t+\t593897\tCCATGGA-----------\n-s\tsimHuman_chr6.simHuman.chr6\t601703\t7\t+\t601863\tCCAGCCA-----------\n-s\tsimRat_chr6.simRat.chr6\t1101\t7\t-\t647215\tTGTGCCA-----------\n-\n-a\n-s\tsimMouse_chr6.simMouse.chr6\t636055\t35\t+\t636262\tATGAACCACTCAAGAACATTATGAGCGTTATAGGG\n-s\tAnc0.Anc0refChr2\t17835\t35\t+\t17989\tATCAACTGCTCGGGAAGATCATCAGCCTCATATGG\n-s\tAnc1.Anc1refChr1\t69613\t35\t+\t69767\tATCAACTGCTCGGGAAGATCATCAGCCTCATATGG\n-s\tAnc2.Anc2refChr1\t142833\t35\t+\t142988\tATCAACTGCTCGGGAAGATCATCAGTCTCATATGG\n-s\tmr.mrrefChr1\t492\t35\t+\t670\tATGAACCACTCAAGAACATTATGAGCCTTATAGGG\n-s\tsimCow_chr6.simCow.chr6\t602467\t34\t+\t602619\tACCAACTGCTCTGGAAGA-TAGCAGTCTCATTTGG\n-s\tsimDog_chr6.simDog.chr6\t593741\t34\t+\t593897\tATCAACTGCCCGGGAAGACCATCAG-CTTGTATTG\n-s\tsimHuman_chr6.simHuman.chr6\t601710\t35\t+\t601863\tATCAACTGGTCCTGAAGATCATCAGCCTCATGTGG\n-s\tsimRat_chr6.simRat.chr6\t647041\t35\t+\t647215\tCAGTACCACTCAAGAACATTATGAGCCTTATAAGG\n-\n-a\n-s\tsimMouse_chr6.simMouse.chr6\t636090\t62\t+\t636262\tACAACATATTATTAACCTCATGGAGACATTGTGGCGACATTGCCAAAGATAGAGATATTGCC\n-s\tAnc0.Anc0refChr2\t17870\t8\t+\t17989\tATAA------------------------------------------------------TGCC\n-s\tAnc1.Anc1refChr1\t69648\t8\t+\t69767\tATAA------------------------------------------------------TGCC\n-s\tAnc2.Anc2refChr1\t142868\t8\t+\t142988\tATAT------------------------------------------------------TGCC\n-s\tmr.mrrefChr1\t527\t33\t+\t670\tACAACATATTATTAACCTCATGGAGAC-----------------------------ATTGCC\n-s\tsimCow_chr6.simCow.chr6\t602502\t8\t+\t602619\tACAG------------------------------------------------------TGCC\n-s\tsimDog_chr6.simDog.chr6\t593775\t8\t+\t593897\tATGT------------------------------------------------------TGCC\n-s\tsimHuman_chr6.simHuman.chr6\t601745\t8\t+\t601863\tATAA------------------------------------------------------TGCC\n-s\tsimRat_chr6.simRat.chr6\t647076\t33\t+\t647215\tACAACACATTGTTAGCCTCATGGAGAC-----------------------------ATTGCC\n-\n-a\n-s\tsimMouse_chr6.simMouse.chr6\t636152\t23\t+\t636262\tAAAGATATATTGAATACTGTTAT\n-s\tAnc0.Anc0refChr2\t17878\t21\t+\t17989\tAAAGATG--ATAAGAACTGTTGT\n-s\tAnc1.Anc1refChr1\t69656\t21\t+\t69767\tAAAGATG--ATAAGAACTGTTGT\n-s\tAnc2.Anc2refChr1\t142877\t21\t+\t142988\tAAAGATC--ATAAGAACTGTTGT\n-s\tmr.mrrefChr1\t560\t23\t+\t670\tAAAGATGTATTAAATACTGTTAT\n-s\tsimCow_chr6.simCow.chr6\t602511\t20\t+\t602619\tAA-GATC--TCAAGAACTGTTGT\n-s\tsimDog_chr6.simDog.chr6\t593786\t21\t+\t593897\tAAAATTC--ATAAGAACTGTTGT\n-s\tsimHuman_chr6.simHuman.chr6\t601753\t21\t+\t601863\tAAAGATG--ATAAGCATTGTTGT\n-s\tsimRat_chr6.simRat.chr6\t647109\t23\t+\t647215\tAAAGATGTATTAAATACTGTTAT\n-\n-a\n-s\tsimMouse_chr6.simMouse.chr6\t636175\t19\t+\t636262\tCCCATGTTATATTCACAAA\n-s\tAnc0.Anc0refChr2\t17901\t19\t+\t17989\tCCCATGTTATATTTAAAAA\n-s\tAnc1.Anc1refChr1\t69679\t19\t+\t69767\tCCCATGTTATATTTAAAAA\n-s\tAnc2.Anc2refChr1\t142900\t19\t+\t142988\tCCCATGTTATATTTAAGAG\n-s\tmr.mrrefChr1\t583\t19\t+\t670\tCCCATGTTATATTCACAAA\n-s\tsimCow_chr6.simCow.chr6\t602533\t19\t+\t602619\tCCCCTGTTATATTTATGAG\n-s\tsimDog_chr6.simDog.chr6\t593809\t19\t+\t593897\tTCCATGTTAGATTCAAGAG\n-s\tsimHuman_chr6.simHuman.chr6\t601776\t19\t+\t601863\tCCCATGTTATATGTAAAAA\n-s\tsimRat_chr6.simRat.chr6\t647132\t19\t+\t647215\tCCCATGTTATATTCACAAA\n-\n-a\n-s\tsimMouse_chr6.simMouse.chr6\t636194\t68\t+\t636262\tCAACTCTCATCCCAACGAATGCTTTGCACACATTAAGACTCACAAATTGAAGACACTGTTGTGAGAAT\n-s\tAnc0.Anc0refChr2\t17921\t68\t+\t17989\tTAACTCTCACCCCAGCAAATGCTTTGTGCATATTGAGACCAACTCATTGAAGACACTGTTATGAGAAT\n-s\tAnc1.Anc1refChr1\t69699\t68\t+\t69767\tTAACTCTCACCCCAGCAAATGCTTTGTGCATATTGAGACCAACTCATTGAAGACACTGTTATGAGAAT\n-s\tAnc2.Anc2refChr1\t142920\t68\t+\t142988\tTAACTCTCACCCCAGCAAATGCTTTGTGTATATTGAGACCAACTCATTGAAGACACTGTTATGAGAAT\n-s\tmr.mrrefChr1\t602\t68\t+\t670\tCAACTCTCATCCCAACAAATGCTTTGTACACATTAAGACTCACAAATTGAAGACACTGTTGTGAGAAT\n-s\tsimCow_chr6.simCow.chr6\t602553\t66\t+\t602619\tAAACCCTCACCCCAGCAAATGCTTTGTGTGC--TGAGACTCACTCATTGAAGACACTGTTATGAAAAT\n-s\tsimDog_chr6.simDog.chr6\t593829\t68\t+\t593897\tTCACTCTCACCCCAGCACATACTTTGTGTATATTGAGACCAACACATTGAAGACACTGCTATGAGAAT\n-s\tsimHuman_chr6.simHuman.chr6\t601796\t67\t+\t601863\tTAGCTCCCAGCCCAGCAAAAGTTTTGTGCAT-TTGAGACCAGCTCACTGAAGACACCATTATGAGAAT\n-s\tsimRat_chr6.simRat.chr6\t647151\t64\t+\t647215\tCAAC-CTCATCCCAACAAATGCTTTGTACACATTAAGACTTACA---TAAAGACATTGTTGTGAGAAT\n-\n'

diff -r 3ff17bad4006 -r c44f824c051a test-data/evolverMammals_both.maf
--- a/test-data/evolverMammals_both.maf Mon Aug 28 23:09:49 2023 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r 3ff17bad4006 -r c44f824c051a test-data/evolverMammals_noroot.hal

Binary file test-data/evolverMammals_noroot.hal has changed

diff -r 3ff17bad4006 -r c44f824c051a test-data/evolverMammals_noroot.maf
--- a/test-data/evolverMammals_noroot.maf Mon Aug 28 23:09:49 2023 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,256420 +0,0 @@\n-##maf version=1 scoring=N/A\n-# hal ((simHuman_chr6:0.144018,(simMouse_chr6:0.084509,simRat_chr6:0.091589)mr:0.271974)Anc1:0.020593,(simCow_chr6:0.18908,simDog_chr6:0.16303)Anc2:0.032898)Anc0;\n-\n-a\n-s\tsimMouse_chr6.simMouse.chr6\t0\t4\t+\t636262\tTTTT\n-s\tAnc0.Anc0refChr9\t0\t4\t-\t35212\tTCTT\n-s\tAnc1.Anc1refChr0\t0\t4\t+\t16026\tTCTT\n-s\tAnc2.Anc2refChr0\t0\t4\t+\t56053\tTCTT\n-s\tmr.mrrefChr0\t0\t4\t+\t130230\tTTTT\n-s\tsimCow_chr6.simCow.chr6\t0\t4\t+\t602619\tTCTT\n-s\tsimDog_chr6.simDog.chr6\t0\t4\t+\t593897\tTCTT\n-s\tsimHuman_chr6.simHuman.chr6\t0\t4\t+\t601863\tTCTT\n-s\tsimRat_chr6.simRat.chr6\t0\t4\t+\t647215\tTTTT\n-\n-a\n-s\tsimMouse_chr6.simMouse.chr6\t4\t33\t+\t636262\tTCAGTTGCAATACCCAACCGGGAGAAACTTTCA\n-s\tAnc0.Anc0refChr9\t4\t33\t-\t35212\tTCTGGTGCAATACCCAATCTGTAGACAGTTTCA\n-s\tAnc1.Anc1refChr0\t4\t33\t+\t16026\tTCTGGTGCAATACCCAATCTGTAGACAGTTTCA\n-s\tAnc2.Anc2refChr0\t4\t33\t+\t56053\tTCTGGTGCACTACCCAATCTGTAGACAGTCTCA\n-s\tmr.mrrefChr0\t5\t33\t+\t130230\tTCAGTTGCAATACCCAACCTGGAGACACTTTCA\n-s\tsimCow_chr6.simCow.chr6\t4\t33\t+\t602619\tTCTGGTGCGCGACCCAATCTGTAGACGGACTTA\n-s\tsimDog_chr6.simDog.chr6\t5\t33\t+\t593897\tTCTGGTGCACTACCCAATCTGTAGACAGTCTCA\n-s\tsimHuman_chr6.simHuman.chr6\t4\t33\t+\t601863\tTCTGGTGCAATAGCCAATCTGCAAACAGTTTCA\n-s\tsimRat_chr6.simRat.chr6\t5\t31\t+\t647215\t--GGCTGCAATACCCAACCTGAAGACATTTTCA\n-\n-a\n-s\tsimMouse_chr6.simMouse.chr6\t37\t60\t+\t636262\tGTGAGCACACCTCAGGTTCCTATATCAAGCAGGCAGTCTTGCATAGCAAATGGTCTCTGG\n-s\tAnc0.Anc0refChr9\t39\t43\t-\t35212\tATGAGCACACCTTATGTGACTATATCAAGCA-----------------CATAGTCTTGCA\n-s\tAnc1.Anc1refChr0\t39\t60\t+\t16026\tATGAGCACACCTTATGTGACTATATCAAGCATACAGTCTTGCCTAGCACATAGTCTTGCA\n-s\tAnc2.Anc2refChr0\t39\t43\t+\t56053\tATGAGCACACCTTATGTGACTATATCAAGCA-----------------CATAGTCTTGCA\n-s\tmr.mrrefChr0\t38\t60\t+\t130230\tGTGAGCACACCTCAGGTTCCTATATCAAGCAGACAGTCTTGCATAGCAAATGGTCTCTGA\n-s\tsimCow_chr6.simCow.chr6\t39\t43\t+\t602619\tCTGAGCACACCTTATGTGATTATATCAAGCA-----------------GATAGTCTTGCA\n-s\tsimDog_chr6.simDog.chr6\t40\t41\t+\t593897\tAT--ACAAACCTTATGTGACTATATCAAGCA-----------------CATGGTCTTGCA\n-s\tsimHuman_chr6.simHuman.chr6\t39\t58\t+\t601863\tATGAGCACACCTTATATGAC--TATCAAGCATACAGTCTTGCCTAGCACACAATCTTGCA\n-s\tsimRat_chr6.simRat.chr6\t36\t60\t+\t647215\tGTGGGCCCACCTCAGGTTCTTATATCAAGCAGACAGTCTTGCGCAACAGATGGTCTCTGA\n-\n-a\n-s\tsimMouse_chr6.simMouse.chr6\t97\t41\t+\t636262\tTAGACGGTGCACTCAATCTATGTGAGGTATAGAAAATAAAG\n-s\tAnc0.Anc0refChr9\t82\t41\t-\t35212\tTAGATTGTGCAATCACTCTATCTGAGAGTCAGAGACCAAAG\n-s\tAnc1.Anc1refChr0\t99\t41\t+\t16026\tTAGATTGTGCAATCACTCTATCTGAGAGTCAGAGACCAAAG\n-s\tAnc2.Anc2refChr0\t82\t41\t+\t56053\tTAGATTGTGCAATGACTCTATCCAAGAGTCAGAGACCAGAG\n-s\tmr.mrrefChr0\t98\t41\t+\t130230\tTAGACGGTGCACTCAATCTATGTGAGGGATAGAAAACAAAG\n-s\tsimCow_chr6.simCow.chr6\t82\t41\t+\t602619\tTTGATTGTGCAATGACTCTATCCAAGAGTCAAAGACCAGAG\n-s\tsimDog_chr6.simDog.chr6\t81\t41\t+\t593897\tTAGATTGTGCAATGACTCTATCCAAGAGTCAGAGGCTGGAG\n-s\tsimHuman_chr6.simHuman.chr6\t98\t41\t+\t601863\tTAGATTGTACAATCTCTCGTTCTGGGAGTCAGAGACCAAAG\n-s\tsimRat_chr6.simRat.chr6\t96\t41\t+\t647215\tTAGACAGTGCACTCAATCTATGTGAAGGATAGAAAACAAAG\n-\n-a\n-s\tsimMouse_chr6.simMouse.chr6\t138\t39\t+\t636262\tGACTACACACATCTCATCAAGTATCCCGTCATATTTGTG\n-s\tAnc0.Anc0refChr9\t127\t37\t-\t35212\tTACT--GCATAGTTCATCGAGTATCCTGGAGTCTTGGTC\n-s\tAnc1.Anc1refChr0\t144\t37\t+\t16026\tTACT--GCATAGTTCATCGAGTATCCTGGAGTCTTGGTC\n-s\tAnc2.Anc2refChr0\t127\t37\t+\t56053\tTACT--GCATAGTTCATTGAGAATCCTGGAGTCTTGGTC\n-s\tmr.mrrefChr0\t139\t37\t+\t130230\tGACT--ACACATCTCATCAAGTATCCTGTCGTATTTGTG\n-s\tsimCow_chr6.simCow.chr6\t126\t36\t+\t602619\tTACG--GCATAGTTTATTG-GAATCCTGGAGTATGGGTC\n-s\tsimDog_chr6.simDog.chr6\t126\t37\t+\t593897\tTATT--ACATAGTTCTCTGAGAATCCTGGAGTCTTTATC\n-s\tsimHuman_chr6.simHuman.chr6\t143\t37\t+\t601863\tTACT--GTGTGGTTGATCGGGTATCCTGGAGTGTTGGTA\n-s\tsimRat_chr6.simRat.chr6\t137\t37\t+\t647215\tGACT--ACTCATCTCATCAAGTATCCTGTCGTATTTGTG\n-\n-a\n-s\tsimMouse_chr6.simMouse.chr6\t177\t9\t+\t636262\tGCAAAACAC\n-s\tAnc0.Anc0refChr9\t175\t9\t-\t35212\tGCAAAGCGC\n-s\tAnc1.Anc1refChr0\t192\t9\t+\t16026\tGCAAAGCGC\n-s\tAnc2.Anc2refChr0\t175\t9\t+\t56053\tGCAAAGCGC\n-s\tmr.mrrefChr0\t187\t9\t+\t130230\tGCAAAACAC\n-s\tsimCow_chr6.simCow.chr6\t173\t9\t+\t602619\tGCAAAGCAC\n-s\tsimDog_chr6.simDog.chr6\t174\t9\t+\t593897\tGCAAAGCGC\n-s\tsimHuman_chr6.simHuman.chr6\t191\t4\t+\t601863\tA'..b'r6\t593734\t7\t+\t593897\tCCATGGA-----------\n-s\tsimHuman_chr6.simHuman.chr6\t601703\t7\t+\t601863\tCCAGCCA-----------\n-s\tsimRat_chr6.simRat.chr6\t1101\t7\t-\t647215\tTGTGCCA-----------\n-\n-a\n-s\tsimMouse_chr6.simMouse.chr6\t636055\t35\t+\t636262\tATGAACCACTCAAGAACATTATGAGCGTTATAGGG\n-s\tAnc0.Anc0refChr2\t17835\t35\t+\t17989\tATCAACTGCTCGGGAAGATCATCAGCCTCATATGG\n-s\tAnc1.Anc1refChr1\t69613\t35\t+\t69767\tATCAACTGCTCGGGAAGATCATCAGCCTCATATGG\n-s\tAnc2.Anc2refChr1\t142833\t35\t+\t142988\tATCAACTGCTCGGGAAGATCATCAGTCTCATATGG\n-s\tmr.mrrefChr1\t492\t35\t+\t670\tATGAACCACTCAAGAACATTATGAGCCTTATAGGG\n-s\tsimCow_chr6.simCow.chr6\t602467\t34\t+\t602619\tACCAACTGCTCTGGAAGA-TAGCAGTCTCATTTGG\n-s\tsimDog_chr6.simDog.chr6\t593741\t34\t+\t593897\tATCAACTGCCCGGGAAGACCATCAG-CTTGTATTG\n-s\tsimHuman_chr6.simHuman.chr6\t601710\t35\t+\t601863\tATCAACTGGTCCTGAAGATCATCAGCCTCATGTGG\n-s\tsimRat_chr6.simRat.chr6\t647041\t35\t+\t647215\tCAGTACCACTCAAGAACATTATGAGCCTTATAAGG\n-\n-a\n-s\tsimMouse_chr6.simMouse.chr6\t636090\t62\t+\t636262\tACAACATATTATTAACCTCATGGAGACATTGTGGCGACATTGCCAAAGATAGAGATATTGCC\n-s\tAnc0.Anc0refChr2\t17870\t8\t+\t17989\tATAA------------------------------------------------------TGCC\n-s\tAnc1.Anc1refChr1\t69648\t8\t+\t69767\tATAA------------------------------------------------------TGCC\n-s\tAnc2.Anc2refChr1\t142868\t8\t+\t142988\tATAT------------------------------------------------------TGCC\n-s\tmr.mrrefChr1\t527\t33\t+\t670\tACAACATATTATTAACCTCATGGAGAC-----------------------------ATTGCC\n-s\tsimCow_chr6.simCow.chr6\t602502\t8\t+\t602619\tACAG------------------------------------------------------TGCC\n-s\tsimDog_chr6.simDog.chr6\t593775\t8\t+\t593897\tATGT------------------------------------------------------TGCC\n-s\tsimHuman_chr6.simHuman.chr6\t601745\t8\t+\t601863\tATAA------------------------------------------------------TGCC\n-s\tsimRat_chr6.simRat.chr6\t647076\t33\t+\t647215\tACAACACATTGTTAGCCTCATGGAGAC-----------------------------ATTGCC\n-\n-a\n-s\tsimMouse_chr6.simMouse.chr6\t636152\t23\t+\t636262\tAAAGATATATTGAATACTGTTAT\n-s\tAnc0.Anc0refChr2\t17878\t21\t+\t17989\tAAAGATG--ATAAGAACTGTTGT\n-s\tAnc1.Anc1refChr1\t69656\t21\t+\t69767\tAAAGATG--ATAAGAACTGTTGT\n-s\tAnc2.Anc2refChr1\t142877\t21\t+\t142988\tAAAGATC--ATAAGAACTGTTGT\n-s\tmr.mrrefChr1\t560\t23\t+\t670\tAAAGATGTATTAAATACTGTTAT\n-s\tsimCow_chr6.simCow.chr6\t602511\t20\t+\t602619\tAA-GATC--TCAAGAACTGTTGT\n-s\tsimDog_chr6.simDog.chr6\t593786\t21\t+\t593897\tAAAATTC--ATAAGAACTGTTGT\n-s\tsimHuman_chr6.simHuman.chr6\t601753\t21\t+\t601863\tAAAGATG--ATAAGCATTGTTGT\n-s\tsimRat_chr6.simRat.chr6\t647109\t23\t+\t647215\tAAAGATGTATTAAATACTGTTAT\n-\n-a\n-s\tsimMouse_chr6.simMouse.chr6\t636175\t19\t+\t636262\tCCCATGTTATATTCACAAA\n-s\tAnc0.Anc0refChr2\t17901\t19\t+\t17989\tCCCATGTTATATTTAAAAA\n-s\tAnc1.Anc1refChr1\t69679\t19\t+\t69767\tCCCATGTTATATTTAAAAA\n-s\tAnc2.Anc2refChr1\t142900\t19\t+\t142988\tCCCATGTTATATTTAAGAG\n-s\tmr.mrrefChr1\t583\t19\t+\t670\tCCCATGTTATATTCACAAA\n-s\tsimCow_chr6.simCow.chr6\t602533\t19\t+\t602619\tCCCCTGTTATATTTATGAG\n-s\tsimDog_chr6.simDog.chr6\t593809\t19\t+\t593897\tTCCATGTTAGATTCAAGAG\n-s\tsimHuman_chr6.simHuman.chr6\t601776\t19\t+\t601863\tCCCATGTTATATGTAAAAA\n-s\tsimRat_chr6.simRat.chr6\t647132\t19\t+\t647215\tCCCATGTTATATTCACAAA\n-\n-a\n-s\tsimMouse_chr6.simMouse.chr6\t636194\t68\t+\t636262\tCAACTCTCATCCCAACGAATGCTTTGCACACATTAAGACTCACAAATTGAAGACACTGTTGTGAGAAT\n-s\tAnc0.Anc0refChr2\t17921\t68\t+\t17989\tTAACTCTCACCCCAGCAAATGCTTTGTGCATATTGAGACCAACTCATTGAAGACACTGTTATGAGAAT\n-s\tAnc1.Anc1refChr1\t69699\t68\t+\t69767\tTAACTCTCACCCCAGCAAATGCTTTGTGCATATTGAGACCAACTCATTGAAGACACTGTTATGAGAAT\n-s\tAnc2.Anc2refChr1\t142920\t68\t+\t142988\tTAACTCTCACCCCAGCAAATGCTTTGTGTATATTGAGACCAACTCATTGAAGACACTGTTATGAGAAT\n-s\tmr.mrrefChr1\t602\t68\t+\t670\tCAACTCTCATCCCAACAAATGCTTTGTACACATTAAGACTCACAAATTGAAGACACTGTTGTGAGAAT\n-s\tsimCow_chr6.simCow.chr6\t602553\t66\t+\t602619\tAAACCCTCACCCCAGCAAATGCTTTGTGTGC--TGAGACTCACTCATTGAAGACACTGTTATGAAAAT\n-s\tsimDog_chr6.simDog.chr6\t593829\t68\t+\t593897\tTCACTCTCACCCCAGCACATACTTTGTGTATATTGAGACCAACACATTGAAGACACTGCTATGAGAAT\n-s\tsimHuman_chr6.simHuman.chr6\t601796\t67\t+\t601863\tTAGCTCCCAGCCCAGCAAAAGTTTTGTGCAT-TTGAGACCAGCTCACTGAAGACACCATTATGAGAAT\n-s\tsimRat_chr6.simRat.chr6\t647151\t64\t+\t647215\tCAAC-CTCATCCCAACAAATGCTTTGTACACATTAAGACTTACA---TAAAGACATTGTTGTGAGAAT\n-\n'

diff -r 3ff17bad4006 -r c44f824c051a test-data/germ_25.fasta.gz

Binary file test-data/germ_25.fasta.gz has changed

diff -r 3ff17bad4006 -r c44f824c051a test-data/hal2maf.maf
--- a/test-data/hal2maf.maf Mon Aug 28 23:09:49 2023 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,30423 +0,0 @@\n-##maf version=1 scoring=N/A\n-# hal (simMouse_chr6:0.084509,simRat_chr6:0.091589)mr;\n-\n-a\n-s\tmr.mrrefChr0\t0\t143\t+\t130230\tTTTTCTCAGTTGCAATACCCAACCTGGAGACACTTTCAGTGAGCACACCTCAGGTTCCTATATCAAGCAGACAGTCTTGCATAGCAAATGGTCTCTGATAGACGGTGCACTCAATCTATGTGAGGGATAGAAAACAAAGGACT\n-s\tsimMouse_chr6.simMouse.chr6\t0\t142\t+\t636262\tTTTT-TCAGTTGCAATACCCAACCGGGAGAAACTTTCAGTGAGCACACCTCAGGTTCCTATATCAAGCAGGCAGTCTTGCATAGCAAATGGTCTCTGGTAGACGGTGCACTCAATCTATGTGAGGTATAGAAAATAAAGGACT\n-s\tsimRat_chr6.simRat.chr6\t0\t141\t+\t647215\tTTTTC--GGCTGCAATACCCAACCTGAAGACATTTTCAGTGGGCCCACCTCAGGTTCTTATATCAAGCAGACAGTCTTGCGCAACAGATGGTCTCTGATAGACAGTGCACTCAATCTATGTGAAGGATAGAAAACAAAGGACT\n-\n-a\n-s\tmr.mrrefChr0\t143\t277\t+\t130230\tACACATCTCATCAAGTATCCTGTCGTATTTGTGCTTTAGACTCAGCAAAACACGCGTACAAATGCACACCTGATGGTACTTGCCTGGAATATGACTCTAGGTTGATCCCTGGCACACAGGCAGGTCAATTCCCGAATGATGGTCTGCTTGTCCAGTTCTAGATAATCATTACATTGGTGAACTCACTAAAACACAGTTAAAATTACAAATCCTTTTTAACCAAGCCTAAAGTACAGAAAGTGAATGTTACCCTTGTGATATGAACCAGTATATAGGG\n-s\tsimMouse_chr6.simMouse.chr6\t144\t259\t+\t636262\tACACATCTCATCAAGTATCCCGTCATATTTGTG-----------GCAAAACACACGTACAAATGCACACTTGATGGTACTTGCCTGGAATATGACTCTAGGTTGATCCCTGGCACACAGGCACATTAATTCCCGAATGATGGTCTGCCTGTCCAGTTCTAGATAAT-GTTACATTGGTGAACT---TAAAACACAG---AAATGACACATCCTTTTTAACCAAGCCTAAAGTACAGAAAGTGAATGTCACCCTTGTTATATAAACCAGTATATAGGG\n-s\tsimRat_chr6.simRat.chr6\t141\t275\t+\t647215\tACTCATCTCATCAAGTATCCTGTCGTATTTGTGCTTTAGACTCAGCAAAACAAGTGTGCAAGTGCACACCTGATTGTACTTGTCTGGAATATGACTCTAGGTTGAGCCCTGGCACACACTCAGGTCAACTCC--AATGATGGTCTGCTTGTCCAATTCTAGATAAACATTACATTGGTGAACTCACTAAAACACAGTTAAAATTACTAATCCTTTTTAGCACAGCCTAAAGTACAGAGAGTGAATGTTACCCTTTTGATATGCATCAGTATATAGGG\n-\n-a\n-s\tmr.mrrefChr0\t420\t89\t+\t130230\tAGCCACTGCCCTCTTAGCATTTATTTGCTGTAAGGTAACTGATGAGCTAAAGTCGTCTAGAATGTATAAGTAAAAGTCTGTAAGCATCC\n-s\tsimMouse_chr6.simMouse.chr6\t404\t89\t+\t636262\tAGCCACTGCTCTCTTAGCATTTATTTGCTGTAAAGGAACTGATGAGCTAAAGTCGTCCAGAATGTATAAGCAGAAATTTGTAACCAGCC\n-s\tsimRat_chr6.simRat.chr6\t416\t88\t+\t647215\tAGCCACTGGCCTCTTAGCATTCATTTGCTGTAAGGTAA-TGATGCGCTAAAGTCATCTAGAATGTATAGGTAAAAGTCTGTAAGCATTG\n-\n-a\n-s\tmr.mrrefChr0\t509\t89\t+\t130230\tTAAAGGCAGCAGCTTTGGTTATGACGCACAATTCAAGACCACCTGCTGGATCCAGCTACATTTAGCAATATTACTGATCTGTTGCACAG\n-s\tsimMouse_chr6.simMouse.chr6\t494\t89\t+\t636262\tTAAAGGCAGCAGCTTTGGTTATAACGCACAATTCAAGACCACCTGCTGGATCCAGCTACATTTAGCAATATTACTGATCTGTTGCACAG\n-s\tsimRat_chr6.simRat.chr6\t504\t46\t+\t647215\tTAAAGGCACCGGCTTTGGTTATGATGCACAATTCAAGACCATCTGC-------------------------------------------\n-\n-a\n-s\tmr.mrrefChr0\t598\t192\t+\t130230\tATCCATCAGGGTGATAGAAATGCAACACACATAACTTGTTGTCCAAGAGGTTAATTAGTGTGACCGGATCTACATCCACCTATCAGTGGTCCTCTCTATTCAAGGCTCAAAAACTAGTAGAGTAATAGGGTCTCCAATAAACTATAAGGGCGATAGGGAACTCTAGCTTTTACTTAGCACAACAGCCTACAG\n-s\tsimMouse_chr6.simMouse.chr6\t585\t192\t+\t636262\tATCCATCAGGGTGATAGAAATGCAACACACATAACTTGTTGTCCAAGAGGTTAATTATTGTAAGCGCATCTACATCCATCTATCAGTGGTCCTCTCTATTCAAGGCTCAAAAACTCGTAGACTATTAGGGTCTCCAATAAACTATAAGGGCGATAGGGAACTCTAGCTTTTACTTAGCACAACAGTCTATAG\n-s\tsimRat_chr6.simRat.chr6\t550\t146\t+\t647215\t------------------------------------------CCA----GTTAATTAGTGTGACTGGATCCACATCCACCTATCAGTGGTCCTCTCTATTCAAAGCTCAAAAACTAGTAGAGTAATAGGGGATCCAATAAACTTTAAGGGCGATAGGGAACTCTAGTTTTTACTTAGCAAAACAGCCTACAG\n-\n-a\n-s\tmr.mrrefChr0\t790\t120\t+\t130230\tCCTGCATCTGGTCACCAGTCACCTTTCTTCTAGCAACAAGGTACAGAGTAGGGCTGTGTGGTGGTGAGTGATGTGTACCTTGGCATGAACCCACTGTAGGTAGCAATACTCCAATTGAAG\n-s\tsimMouse_chr6.simMouse.chr6\t777\t120\t+\t636262\tCCTACAACTGGTCACCAGTCACTTTTCTTCTAGCAACAAGGTACAGAGGAGGGCTGTGTGGTGGTGAGTGATGTACACCTTGGCATGAACCCACTGTAGGTAGCAATACTCCAACTGAAG\n-s\tsimRat_chr6.simRat.chr6\t703\t120\t+\t647215\tCCTGGATCTGGTCATCTGTCACCTTTCTTCCAGCAACAAGATACAGAGTAGAGCTGTGGGGTGGTTAGTCATGCGTACCTTAGCATGAGCCCACTGTAGGTAGCAATCCTCCAATTGAAG\n-\n-a\n-s\tmr.mrrefChr0\t910\t506\t+\t130230\tGTTAACCCAAGGAGAAATGCAAATGGGAGTCCGTGCTATTGCAAAATTGTTATATATTCAATTTACTGGCCTTAACTGCATTCCCCGCAGTATTACATACCAATAACCCACATGGTCTCTAAAGACTCTGTTTCGCTTTGGATATTGACTCTAATCTATGTGGCGAAGCACACCCTTAAACTAATCTTCACCTTTCAAGTAATCTTGTGTCTCTATTTGCACAGAGTATGATTATTGTGGGATTGACAGGAGCACTTGTTGGTAATTACAATCagattggattccatattgctcattcagttatcaggatgcaatatgactcaagtagtcccaggtttta'..b'ATAAACTTAACTGTTACCTCTCACTAGATGGGATCATATGGTCTAGTTTTCAATTTCAGGCTACATTTAGGTTGGTTCAGCAGCTCCAATTGAGGTGTTTCCCGAGTGTCAGGTGGTGCTTTTGACAAAG-----------GATATGATACAGATGTCCTGCCAGTGGGCTAAGCACAATTTAAGTGTAAAC----CAGTCATA-ATATTTTAGACCAGTACAAAAATAAGTCATGTAAGCCATTTTTAATATTCCAACACACACAAACTTTACAACTGTAATGTCTCT\n-s\tsimRat_chr6.simRat.chr6\t447929\t832\t+\t647215\tTAGTCCATATCCAGCAGCCCATAACAACCAAAATGAATGTACAAAGTACACAAGATTCCT-TAAAACCAGCAGCACAGACAGTACAGGTTCCACCTGCTGCAGTGTGCTGGTTATTTGGAACTAGATGAAATGCCCAGGGGATGAATGGTTTCTTAGCGAACAACAATACTACAAAGGTTACCAGAAGTGGATTGCCTAATGCTAAAACATTCATGTTTGTTTCATCTGTTCTCTCTATTTGAATCAAGCCCACAAAAGGAAAAATGGAAAGAGAAGACACTAACTTTAAGGAAAGGACTATTGCACTACTGTGCCAGTTTATGTGAAGGACACTTTGTATCAGTTATTGGAGATACTATTCTGTTCCTCATTGTCATGACACCAAAGGCCCCCAACTCACTTCTTCATTCTCCTCTTCATTTGTGAATGCATATATGTGTTTCAAGAAGCTGTTGCTTTGCTGTACTTGCAGCACTCATATTGTTA-TTTGCCACATGAATTAATTGTATGTTTAAGTTTAATACTTAACCTGTTGAAGGTTCTGATGCTTAACTGATCTGTTACCTCTCTCAAGAAGGGATCATATGGTGACGTCTTCAATTTCAGGCTCCATCTAGG-TGGTTCCGCAGCTCCAATTGA---GTTTCCCAAGTATCTGGCGGTGCTTTTGACACAGCTAGTACTTTTGGTAGGATAGAGTTGTCCTGCCAGTGAACTAACCACATTTTAAGTATCAACAACTCAGTCATAGGTAATTTAGACCAGTGTAAAAATGAGTCATGTAAGCCGTTTTTAATATTCCAACGCACACAGACTATACAATTGTAATATCTCT\n-\n-a\n-s\tmr.mrrefChr5\t293926\t271\t+\t294542\tCAAAAAACCAAGTTTTAAGGTTTCGTCAAGTGAACAGGGACACTTATCATACATGCAATCAGATTGTCTGTATTTTAAGAATACCAGTGTTTTTGGTGGATTCATCCAAACCTCAGGTTGACTAGGTATTTGCTGTGGAGTAAGTACATGCATATGACATTAATATCATATTAAGGACTTCTGTAGTATAATGTGTAACCATTGACTTGACTAATATGTAGTGCAAGCTTGTTTACTATCCACATTACCTTCCATCAACTGGGAATTCATT\n-s\tsimMouse_chr6.simMouse.chr6\t440437\t271\t+\t636262\tCAAAAAACCAAGTTTTAAGGTTTCGTCAAGTTAACAGGGACACTTATCATACATGCAATCAGATTGTCTGTATTTTAAGAATACCAGTGTTTTTGGTGGATTCATCCAAACCTCAGGTTGACTAGGTATTTGCTGTGGAGTAAGTACATGCATATGACATTAATATCATATTAAGGACTTCTGTAGTATAATGTGTAACCATTGACTTGACTAATATGTAGTGCAAGCTTGTTTACTATCCACATTACCTTCCATCAACTGGGAATTCATT\n-s\tsimRat_chr6.simRat.chr6\t448779\t271\t+\t647215\tCAAAAAACTAAGTTTTACGGTTTCGTCAGGTGAACAGGGAGACTTATCAGACATGCAGTCAGATTCACTGTATTTTGAAAGTATCAGTGCTTTTGCTGGATTCATCCAATTCTCAGGTTGACAAGGAATTTGCAGTGAAGTCAGTACAGGCACATAACACTAATGTCATATTAGGGACTTCTGTAATAAAATGTGTAACCATTCACTTGACTGACATGTAGTGCAAGCTTGTTTACTATCTACACTACCTTCCATCAACTAGGAATGCGTT\n-\n-a\n-s\tmr.mrrefChr5\t294197\t5\t+\t294542\tATGCT\n-s\tsimMouse_chr6.simMouse.chr6\t440708\t5\t+\t636262\tATGCT\n-s\tsimRat_chr6.simRat.chr6\t449051\t5\t+\t647215\tATGCT\n-\n-a\n-s\tmr.mrrefChr5\t294202\t6\t+\t294542\tATGAGG\n-s\tsimMouse_chr6.simMouse.chr6\t440713\t6\t+\t636262\tATGAGG\n-s\tsimRat_chr6.simRat.chr6\t449058\t6\t+\t647215\tATGACG\n-\n-a\n-s\tmr.mrrefChr5\t294208\t58\t+\t294542\tTGCTGTTCAAGGTGCTGATGATTTTAGGGAGTGCCTTAACCCTGAAAGTTCCCAATAG\n-s\tsimMouse_chr6.simMouse.chr6\t440719\t58\t+\t636262\tTGCTGTTCAAGGTGCTGATGATTTTAGGGAGTGCCTTAACCCTGAAAGTTCCCAATAG\n-s\tsimRat_chr6.simRat.chr6\t449136\t58\t+\t647215\tTGCTGTTCGAAGTGCTGCTGACTTTAAGAAGTGCCTTAACCCCCAGAGCTCCCAATAG\n-\n-a\n-s\tmr.mrrefChr5\t294266\t49\t+\t294542\tGTTGGAGGGAATCAGCATTGTCTTCTTGCCTTAACAGACTATCAAACAA\n-s\tsimMouse_chr6.simMouse.chr6\t440777\t49\t+\t636262\tGTTGGAGGGAATCAGCATTGTCTTCTTGCCTTAACAGACTATCAAACAA\n-s\tsimRat_chr6.simRat.chr6\t449197\t49\t+\t647215\tGGAGGGGGGAATCAGCATTGTCTTCTTATCTTAACAGACTATCAAACAA\n-\n-a\n-s\tmr.mrrefChr5\t294315\t153\t+\t294542\tACTTAACCTGTGGGCATCCAAATCTTTAAATCTGGGATTGAATGATATTCATTGAAACTTGTCCTTCAAGAGCCCTCATCTCACTCCAACACCGCTAGTGTCGTTTGGGTCAACTCTCACATGTTGAGGATCCAGAGCCACCTGCTCAGAGCG\n-s\tsimMouse_chr6.simMouse.chr6\t440826\t153\t+\t636262\tACTTAACCTGTGGGCATCCAAATCTTTAAATCTGGGATTGAATGATATTCATTGAAACTTGTCCTTCAAGAGCCCTCATCTCACTCCAACACCGCTAGTGTCGTTTGGGTCAACTCTCACATGTTGAGGATCCAGAGCCACCTGCTCAGAGCG\n-s\tsimRat_chr6.simRat.chr6\t449310\t153\t+\t647215\tGCTTAACCTGTGGGCATGCAACTCTTTAAATCTGGGGCTGAGTGGTTTTCATCAAAACTTGTCTTGCAAGAGCCAGTATCTGACTCCAACAGTGCTAGTATCATTTGGGTGGACTCTCACATGTTGAAAATCCGAAGCCATCCGCTCTGGGCA\n-\n-a\n-s\tmr.mrrefChr5\t294468\t74\t+\t294542\tTTTCTGTCAGTGCATTTGCATGTATGATGGTGACAGTAACAAAGAAAATCTGATACATGTGCTGAAGAATGGTG\n-s\tsimMouse_chr6.simMouse.chr6\t440979\t74\t+\t636262\tTTTCTGTCAGTGCATTTGCATGTATGATGGTGACAGTAACAAAGAAAATCTGATACATGTGCTGAAGAATGGTG\n-s\tsimRat_chr6.simRat.chr6\t449482\t74\t+\t647215\tTTTCTATCAGTGCATTTGCATATATTGTCCTAACAGAAACAAAGAGGATCAGATACAATTGCTGAAGAGTGGTG\n-\n'

diff -r 3ff17bad4006 -r c44f824c051a test-data/pens_25.fasta.gz

Binary file test-data/pens_25.fasta.gz has changed

diff -r 3ff17bad4006 -r c44f824c051a test-data/set_reference.maf
--- a/test-data/set_reference.maf Mon Aug 28 23:09:49 2023 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,2551 +0,0 @@\n-##maf version=1 scoring=N/A\n-# hal (simCow_chr6:1,simDog_chr6:1,simHuman_chr6:1,simMouse_chr6:1,simRat_chr6:1,_MINIGRAPH_:1)Anc0;\n-\n-a\n-s\tsimMouse_chr6.simMouse.chr6\t0\t1000\t+\t636262\tTTTTTCAGTTGCAATACCCAACCGGGAGAAACTTTCAGTGAGCACACCTCAGGTTCCTATATCAAGCAGGCAGTCTTGCATAGCAAATGGTCTCTGGTAGACGGTGCACTCAATCTATGTGAGGTATAGAAAATAAAGGACTACACACATCTCATCAAGTATCCCGTCATATTTGTGGCAAAACACACGTACAAATGCACACTTGATGGTACTTGCCTGGAATATGACTCTAGGTTGATCCCTGGCACACAGGCACATTAATTCCCGAATGATGGTCTGCCTGTCCAGTTCTAGATAATGTTACATTGGTGAACTTAAAACACAGAAATGACACATCCTTTTTAACCAAGCCTAAAGTACAGAAAGTGAATGTCACCCTTGTTATATAAACCAGTATATAGGGTAGCCACTGCTCTCTTAGCATTTATTTGCTGTAAAGGAACTGATGAGCTAAAGTCGTCCAGAATGTATAAGCAGAAATTTGTAACCAGCCTTAAAGGCAGCAGCTTTGGTTATAACGCACAATTCAAGACCACCTGCTGGATCCAGCTACATTTAGCAATATTACTGATCTGTTGCACAGCAATCCATCAGGGTGATAGAAATGCAACACACATAACTTGTTGTCCAAGAGGTTAATTATTGTAAGCGCATCTACATCCATCTATCAGTGGTCCTCTCTATTCAAGGCTCAAAAACTCGTAGACTATTAGGGTCTCCAATAAACTATAAGGGCGATAGGGAACTCTAGCTTTTACTTAGCACAACAGTCTATAGCCTACAACTGGTCACCAGTCACTTTTCTTCTAGCAACAAGGTACAGAGGAGGGCTGTGTGGTGGTGAGTGATGTACACCTTGGCATGAACCCACTGTAGGTAGCAATACTCCAACTGAAGTATTAGCCCGAGGAGAAATGCAAGTGCGAGTCCGTGCTATTGCAAAATTGGTATATATTCAATTTACTGGCCTTAGCTGCATTCCCCACAGTATTACATACCA\n-s\tAnc0.Anc0refChr3\t0\t1000\t+\t636262\tTTTTTCAGTTGCAATACCCAACCGGGAGAAACTTTCAGTGAGCACACCTCAGGTTCCTATATCAAGCAGGCAGTCTTGCATAGCAAATGGTCTCTGGTAGACGGTGCACTCAATCTATGTGAGGTATAGAAAATAAAGGACTACACACATCTCATCAAGTATCCCGTCATATTTGTGGCAAAACACACGTACAAATGCACACTTGATGGTACTTGCCTGGAATATGACTCTAGGTTGATCCCTGGCACACAGGCACATTAATTCCCGAATGATGGTCTGCCTGTCCAGTTCTAGATAATGTTACATTGGTGAACTTAAAACACAGAAATGACACATCCTTTTTAACCAAGCCTAAAGTACAGAAAGTGAATGTCACCCTTGTTATATAAACCAGTATATAGGGTAGCCACTGCTCTCTTAGCATTTATTTGCTGTAAAGGAACTGATGAGCTAAAGTCGTCCAGAATGTATAAGCAGAAATTTGTAACCAGCCTTAAAGGCAGCAGCTTTGGTTATAACGCACAATTCAAGACCACCTGCTGGATCCAGCTACATTTAGCAATATTACTGATCTGTTGCACAGCAATCCATCAGGGTGATAGAAATGCAACACACATAACTTGTTGTCCAAGAGGTTAATTATTGTAAGCGCATCTACATCCATCTATCAGTGGTCCTCTCTATTCAAGGCTCAAAAACTCGTAGACTATTAGGGTCTCCAATAAACTATAAGGGCGATAGGGAACTCTAGCTTTTACTTAGCACAACAGTCTATAGCCTACAACTGGTCACCAGTCACTTTTCTTCTAGCAACAAGGTACAGAGGAGGGCTGTGTGGTGGTGAGTGATGTACACCTTGGCATGAACCCACTGTAGGTAGCAATACTCCAACTGAAGTATTAGCCCGAGGAGAAATGCAAGTGCGAGTCCGTGCTATTGCAAAATTGGTATATATTCAATTTACTGGCCTTAGCTGCATTCCCCACAGTATTACATACCA\n-\n-a\n-s\tsimMouse_chr6.simMouse.chr6\t1000\t1000\t+\t636262\tATAACCCACATGGTCTCTAAAGACTCTGTTTCGCTTTGGATGTTGACTCTCATCTATGGGCCAAACACACCTTTAAACTAATCTTCACCTTTCAAGTGATCTTGTGTCTCTATTTGCACAGAGTAAGATTATTGTGCGATTGATAGGAGCACTTGTTGGTAATTACTATCagactggattccatattgctcactcagttatcaggatgcaatatgactcaagtagtcccaggttttaaaccatcagAGCTCACTGATAGGGGTTTGCTGGGAACCTATATTGATCCAGGGAAGAGGCCACCTGCAACATGTGCGCCTTGTCTACTACATGTAGGATTGAAGTTGTCAAGATCGAATCTTGCAGAGAATCGGATACTTTGTATAGTTATCTCATTCTCTCCTCCACCACATTCTCTCCTCCACCACTACCTCTCAAATAGCACCTTCTGAATGCCAACTAGTACTCTTATTTTGCTTTTTCAGATCTACAATTAGATGTGTTAGGTGCTCCCATATAGGGACTGCTCCACCATGAAAAAGACTGAACACCATGGTGTATAGCATCCTTTGACTGATGTTCTACAGTATTGTTTAAACATTACCTGTTCTAGTACACTCCATGGTACCTTGACTACATTCTGAGGGATTCCTTCTGTAATGTTAACACTGTTCCTAATGACTTATAATATAGTTTACTAGATAGTATAATTTACTAGGTGAGGAGTCATGTTGCTCCCACAGACAAAATTAATTCAACAGGAAGTCTGTAACCCAATACAATGCTGGCAGTGAAGTATGATTAGTGCTGTCAATTAATCATGATTAAATGGCCTCCTTGAACGGGCTAGACGTTTTGGAGCTGTAGTATACCTTCTAGTTCTTTAATGTTTTAGCTTAATTAAACATATGCTATTGTGATTCACACTTTTCTTTGGCCTATCTGCATTATACATTGAGGTTGAGAGTACAATAACACTTCTGTTGTGTGAATTGTACTGATA\n-s\tAnc0.Anc0refChr3\t1000\t1000\t+\t636262\tATAACCCACATGGTCTCTAAAGACTCTGTTTCGCTTTGGATGTTGACTCTCATCTATGGGCCAAACACACCTTTAAACTAATCTTCACCTTTCAAGTGATCTTGTGTCTCTATTTGCACAGAGTAAGATTATTGTGCGATTGATAGGAGCACTTGTTGGTAATTACTATCagactggattccatattgctcactcagttatcaggatgcaatatgactcaagtagtcccaggttttaaaccatcagAGCTCACTGATAGGGGTTTGCTGGGAACCTATATTGATCCAGGGAAGAGGCCACCTGCAACATGTGCGCCTTGTCTACTACATGTAGGATTGAAGTTGTCAAGATCGAATCTTGCAGAGAATCGGATACTTTGTATAGTTATCTCATTCTCTCCTCCACCACATTCTCTCCTCCACCACTACCTCTCAAATAGCACCTTCTGAATGCCAACTAGTACTCTTATTTTGCTTTTTCAGATCTACAATTAGATGTGTTAGGTGCTCCCATATAGGGACTGCTCCACCATGAAAAAGACTGAACACCATGGTGTATAGCATCCTTTGACTGATGTTCTACAGTATTGTTTAAACATTACCTGTTCTAGTACACTCCATGGTACCTTGACTACATTCTGAGGGATTCCTTCTGTAATGTTAAC'..b'CCAGGCCAGTTGCATCGGTTGGTTGTTTTTTCTGATTGGGATGGGATGTGGTCCCATATGTAGCAAGCAATGTCACAGCAGGCGATGAATGGCACATAGTTGGAGGTTCAAAACTCAGCTAGGCTGTTCTTTTAGCATTGAGCACAAGATCGCTTAGAGGGGAGTGTACATAAAATGGGTCCATTCCTCAACAATTTAACAGACTACTCACCCACAATTTAACAGACTACTC\n-s\tAnc0.Anc0refChr3\t634000\t1000\t+\t636262\tATGTGAGACTTTGGAGCGAGCGGCTGTCCTCGCCTTAACAGGGGACACACATGGTGCGTTGATTTATGTACTATCTTGCCGGACAGTCGATACTATTTGTCTACCTTTTAACGGTACTTAGACTTTGTACAGCGCCTCGTGCAAATCTCCAAAAAAAGGCAAACACAGCCATGTACACACAATTAGTGCTTGGCTATGACCCTTCCCTGCACGACCATGTACAAACAGTCAGTGCTTGGCTACACTTGCCCCACAAGTTTGCCCTGCATGATGAAGTGATCTTGGCGCGCACATTGTAGATCCCCTCTCTAGATTTGTGCACTGTCAAGTGATGATAGTCCTTCATGTACATTGTCTTTGTGAAGCCATTTTTTTGGCTCAGCATTCTAGGCTGCTTCAAGTTCCATTTACCAATACACTCACATTTACAATTCTATTTTACATCTCGAGTTGGATAAGATTAGACCTCCTAACAGGTGCTGCCCTCCTTACATTTATAATTAGTAGCACCTGGTATATTACTTCCCAGCTATGCATGAACCGCTTGTGTGAGGTGGGAAGACTCCTTCTGTGATCACTATTGCATCCATGCTGTGAAGCTTTGCCTGTCAGTGGACCGCAATTCCTCTTGGTCAATCACTGTGGCCAGTCCAACCCACCTGTTGGTCAGAAAGGAGACCACGCCAAGCTGGGATTCAAGGCAATCAGGTGTTGGATCCCCCCACTTAATTGGCAAAGATCAGTGCTATGCAGATCCACACTACACACCCAGGCCAGTTGCATCGGTTGGTTGTTTTTTCTGATTGGGATGGGATGTGGTCCCATATGTAGCAAGCAATGTCACAGCAGGCGATGAATGGCACATAGTTGGAGGTTCAAAACTCAGCTAGGCTGTTCTTTTAGCATTGAGCACAAGATCGCTTAGAGGGGAGTGTACATAAAATGGGTCCATTCCTCAACAATTTAACAGACTACTCACCCACAATTTAACAGACTACTC\n-\n-a\n-s\tsimMouse_chr6.simMouse.chr6\t635000\t1000\t+\t636262\tACCCTACTTTGGTCACGGCTCTATTTAGTTGATATGAGGGAGGAGCAGGGAATCTCGATGTAAAATGATCGAGAAAGTGTCAGTTATCTCAAAAGATTAAACTAAAGCACAGGTTTGAGTAAGCACAGATTTGAGTACAACTTTGTATTTGTAGACAATAGGTTAGCCTGCTCTGGGAGAGAGTTACTAGTTTCTCCCCATAGAAGATAAGTTCCACATATTTACTTGTATATATGTAGTTTAATGATCCCCATGTCAGAAAAGCAAGAAGTGGCTTCTTAGAAACTTGTTTCTTGATTGGAGACTTGTGTGTGTCATCTCTCTGTCATGTACATGGCTGCTTGCCTTTTATTGGAGCTTTGCACGAGACACTATGTGAAATCTAAACAACATAAAGCTAAAATCTAAAATTCTTTGCAAATAGTGGGCACGAAAGTCGTTATAACCAGTGAGTGCTACATCGTACTGTCTGGGCCCACGGTCATGATTCGCTCAAGACGATTTGCTAACTGAGCGCTCTGGTATGCGACCGCCTTGCGTACGCTTTGTTCACGACTTCGAAGTCTCTGGATTTACTATGTGTCCATGGAGTTATGACAGGTTTGAGTCTCCAAACACCAGGAATCTGTTTGATCCTGAGGGTTTGTAAAAGGGACTCTTGTCTCTACTAGTTGCCTCATCAGCCAGCAGATTATCTGTGCTTGATACCTGCCATTAGTGTGAAATGGCTATTCTTACTGTAACCCAATTGAGTAGTTATGTGATGTAGTGGCCATCCTGATAACAGACGAGATGCCATGGATTAAAAGTGAAAAATTTAAAACTTATCTGAACACAAGATGAGAACCTATAAGTTGGCCAAAGACAGTGAGAAATACCCTGAACCAACCTAGGTGTCAACAATTTCTACAGTTCGGTGCCTAAGATCCAAGAGAGGCCCAGTCCGTTTTGACCCCTTTGCTAGCTGTAACTACGATATTGTGATGTTTGGCAGTATCAC\n-s\tAnc0.Anc0refChr3\t635000\t1000\t+\t636262\tACCCTACTTTGGTCACGGCTCTATTTAGTTGATATGAGGGAGGAGCAGGGAATCTCGATGTAAAATGATCGAGAAAGTGTCAGTTATCTCAAAAGATTAAACTAAAGCACAGGTTTGAGTAAGCACAGATTTGAGTACAACTTTGTATTTGTAGACAATAGGTTAGCCTGCTCTGGGAGAGAGTTACTAGTTTCTCCCCATAGAAGATAAGTTCCACATATTTACTTGTATATATGTAGTTTAATGATCCCCATGTCAGAAAAGCAAGAAGTGGCTTCTTAGAAACTTGTTTCTTGATTGGAGACTTGTGTGTGTCATCTCTCTGTCATGTACATGGCTGCTTGCCTTTTATTGGAGCTTTGCACGAGACACTATGTGAAATCTAAACAACATAAAGCTAAAATCTAAAATTCTTTGCAAATAGTGGGCACGAAAGTCGTTATAACCAGTGAGTGCTACATCGTACTGTCTGGGCCCACGGTCATGATTCGCTCAAGACGATTTGCTAACTGAGCGCTCTGGTATGCGACCGCCTTGCGTACGCTTTGTTCACGACTTCGAAGTCTCTGGATTTACTATGTGTCCATGGAGTTATGACAGGTTTGAGTCTCCAAACACCAGGAATCTGTTTGATCCTGAGGGTTTGTAAAAGGGACTCTTGTCTCTACTAGTTGCCTCATCAGCCAGCAGATTATCTGTGCTTGATACCTGCCATTAGTGTGAAATGGCTATTCTTACTGTAACCCAATTGAGTAGTTATGTGATGTAGTGGCCATCCTGATAACAGACGAGATGCCATGGATTAAAAGTGAAAAATTTAAAACTTATCTGAACACAAGATGAGAACCTATAAGTTGGCCAAAGACAGTGAGAAATACCCTGAACCAACCTAGGTGTCAACAATTTCTACAGTTCGGTGCCTAAGATCCAAGAGAGGCCCAGTCCGTTTTGACCCCTTTGCTAGCTGTAACTACGATATTGTGATGTTTGGCAGTATCAC\n-\n-a\n-s\tsimMouse_chr6.simMouse.chr6\t636000\t262\t+\t636262\tCCTCACACTGAGACTTTAGATCTGGAGCAAGTACTTTTGTGCCATAGGCCCCTGGATGAACCACTCAAGAACATTATGAGCGTTATAGGGACAACATATTATTAACCTCATGGAGACATTGTGGCGACATTGCCAAAGATAGAGATATTGCCAAAGATATATTGAATACTGTTATCCCATGTTATATTCACAAACAACTCTCATCCCAACGAATGCTTTGCACACATTAAGACTCACAAATTGAAGACACTGTTGTGAGAAT\n-s\tAnc0.Anc0refChr3\t636000\t262\t+\t636262\tCCTCACACTGAGACTTTAGATCTGGAGCAAGTACTTTTGTGCCATAGGCCCCTGGATGAACCACTCAAGAACATTATGAGCGTTATAGGGACAACATATTATTAACCTCATGGAGACATTGTGGCGACATTGCCAAAGATAGAGATATTGCCAAAGATATATTGAATACTGTTATCCCATGTTATATTCACAAACAACTCTCATCCCAACGAATGCTTTGCACACATTAAGACTCACAAATTGAAGACACTGTTGTGAGAAT\n-\n'

diff -r 3ff17bad4006 -r c44f824c051a test-data/vulg_25.fasta.gz

Binary file test-data/vulg_25.fasta.gz has changed

diff -r 3ff17bad4006 -r c44f824c051a test-data/within.hal

Binary file test-data/within.hal has changed