Galaxy |

Changeset 0:85f68b344286 (2022-04-04)

Next changeset 1:1bc1199f0ff4 (2022-06-22)

Commit message:
"planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"

added:
README.rst
cactus_cactus.xml
macros.xml
test-data/bh1.fasta.gz
test-data/bh2.fasta.gz
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/simCow_chr6.fasta
test-data/simDog_chr6.fasta
test-data/simHuman_chr6.fasta
test-data/simMouse_chr6.fasta
test-data/simRat_chr6.fasta
test-data/test_tree.nhx
test-data/vulg_25.fasta.gz
test-data/within.hal

diff -r 000000000000 -r 85f68b344286 README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst Mon Apr 04 06:27:44 2022 +0000

@@ -0,0 +1,18 @@
+Cactus
+======
+
+This suite contains a wrapper for the
+`Cactus <github.com/comparativeGenomicsToolkit/cactus>`__ whole-genome
+aligner and another wrapper for exporting the data it generates.
+
+Requirements
+------------
+
+The developers provide an official Docker container. However, the Docker
+container won’t run unless ``/etc/passwd`` is mounted (`see this
+issue <https://github.com/ComparativeGenomicsToolkit/cactus/issues/677>`__).
+Because of this, it is recommended to run Cactus using Singularity.
+
+Cactus uses a lot of RAM. We have tested it on Galaxy using 24 GB of RAM
+for a progressive alignment of three chromosome-level, 150 megabase
+genomes.

diff -r 000000000000 -r 85f68b344286 cactus_cactus.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cactus_cactus.xml Mon Apr 04 06:27:44 2022 +0000

[

b'@@ -0,0 +1,268 @@\n+<tool id="cactus_cactus" name="Cactus" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">\n+ <description>whole-genome multiple sequence alignment.</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="xrefs"/>\n+ <expand macro="requirements"/>\n+ <command detect_errors="exit_code"><![CDATA[\n+ ## Check the FASTA headers\n+ ## This is only necessary in pangenome mode\n+ #if $aln_mode.aln_mode_select == \'intraspecies\':\n+ #for $seq in $in_seqs:\n+ if\n+ #if $seq.fasta.is_of_type(\'fasta.gz\'):\n+ zgrep\n+ #else\n+ grep\n+ #end if\n+ "^>" $seq.fasta | grep -q "[[:space:]]" ; then\n+ echo "Error parsing input FASTA." ;\n+ echo "Pangenome mode fails if there are spaces in the header." ;\n+ echo "Please remove them with the NormalizeFasta tool." ;\n+ exit 1 \n+ ; fi &&\n+ #end for\n+ #end if\n+\n+ ## Set up seqfile\n+ \n+ #if $aln_mode.aln_mode_select == \'interspecies\':\n+ cat $aln_mode.in_tree >> seqfile.txt &&\n+ #end if\n+ #set seq_line = \'\'\n+ #for $seq in $in_seqs:\n+ #set seq_fn = str($seq.label) + \'.\' + $seq.fasta.ext\n+ ln -s \'$seq.fasta\' \'$seq_fn\' &&\n+ printf \'%s %s\\n\' \'$seq.label\' \'$seq_fn\' >> seqfile.txt \n+ #set seq_line += $seq_fn + \' \'\n+ &&\n+ #end for\n+\n+ ## Run cactus\n+\n+ #if $aln_mode.aln_mode_select == \'intraspecies\':\n+ ## If we\'re doing a pangenome, we need to run the steps manually\n+ minigraph -xggs\n+ -t \\${GALAXY_SLOTS:-4}\n+ $seq_line\n+ > pangenome.gfa\n+ &&\n+ cactus-graphmap\n+ --maxCores \\${GALAXY_SLOTS:-4}\n+ --maxMemory \\${GALAXY_MEMORY_MB:-8192}M\n+ ./jobStore\n+ ./seqfile.txt\n+ pangenome.gfa\n+ pangenome.paf \n+ --outputFasta pangenome.gfa.fa\n+ --binariesMode local\n+ --workDir ./\n+ &&\n+ cactus-align\n+ --maxCores \\${GALAXY_SLOTS:-4}\n+ --maxMemory \\${GALAXY_MEMORY_MB:-8192}M\n+ ./jobStore\n+ ./seqfile.txt\n+ pangenome.paf \n+ alignment.hal\n+ --pangenome\n+ --pafInput\n+ --binariesMode local\n+ --workDir ./\n+ #else if $aln_mode.aln_mode_select == \'interspecies\':\n+ ## Run cactus normally\n+ cactus \n+ --maxCores \\${GALAXY_SLOTS:-4}\n+ --maxMemory \\${GALAXY_MEMORY_MB:-8192}M\n+ jobStore seqfile.txt alignment.hal \n+ --binariesMode local \n+ --workDir ./\n+ #end if\n+\n+ ]]></command>\n+ <inputs>\n+ <conditional name="aln_mode">\n+ <param name="aln_mode_select" type="select" label="Alignment mode" help="The taxonomic relationship between input genomes. If genomes are from multiple individuals of the same species, select \'Within-species\'">\n+ <option value="interspecies" selected="true">Between-species</option>\n+ <option value="intraspecies">Within-species</option>\n+ </param>\n+ <when value="interspecies">\n+ <param name="in_tree" type="data" format="nhx" label="Guide tree" help="Phylogenetic tree in Newick format. Required by Cactus to achieve linear scaling with number of input genomes" />\n+ </when>\n+ <when value="intraspecies">\n+ </when>\n+ </conditional>\n+ <repeat name="in_seqs" title="Input genome">\n+ <param name="label" type="text" value="" label="Genome Label" help="NO SPACES. Must match a label in the guide tree.">\n+ </param>\n+ '..b' <param name="fasta" value="simRat_chr6.fasta"/>\n+ </repeat>\n+ <output name="out_hal">\n+ <assert_contents>\n+ <has_size value="2119332" delta="200000" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ \n+ <test expect_num_outputs="1">\n+ <conditional name="aln_mode">\n+ <param name="aln_mode_select" value="intraspecies"/>\n+ </conditional>\n+ <repeat name="in_seqs">\n+ <param name="label" value="germ_25"/>\n+ <param name="fasta" value="germ_25.fasta.gz"/>\n+ </repeat>\n+ <repeat name="in_seqs">\n+ <param name="label" value="vulg_25"/>\n+ <param name="fasta" value="vulg_25.fasta.gz"/>\n+ </repeat>\n+ <repeat name="in_seqs">\n+ <param name="label" value="pens_25"/>\n+ <param name="fasta" value="pens_25.fasta.gz"/>\n+ </repeat>\n+ <output name="out_hal">\n+ <assert_contents>\n+ <has_size value="7204260" delta="200000" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ \n+ <test expect_exit_code="1" expect_failure="true">\n+ <conditional name="aln_mode">\n+ <param name="aln_mode_select" value="intraspecies"/>\n+ </conditional>\n+ <repeat name="in_seqs">\n+ <param name="label" value="badheader1"/>\n+ <param name="fasta" value="bh1.fasta.gz"/>\n+ </repeat>\n+ <repeat name="in_seqs">\n+ <param name="label" value="badheader2"/>\n+ <param name="fasta" value="bh2.fasta.gz"/>\n+ </repeat>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+**What it does**\n+\n+`Cactus <https://github.com/ComparativeGenomicsToolkit/cactus>`__ is a\n+reference-free whole-genome multiple alignment program. It can be used\n+to progressively align a large number of genomes.\n+\n+**Usage**\n+\n+**Between-species mode**\n+\n+If you are aligning genomes from **multiple species**, you need to\n+provide a guide tree in Newick format. Cactus uses the guide tree to\n+progressively align genomes, meaning that it doesn\xe2\x80\x99t need to align all\n+possible pairs of genomes.\n+\n+A Newick-formatted tree for human, chimp and gorilla genomes looks like\n+this:\n+\n+::\n+\n+ (((human:0.006,chimp:0.006667):0.0022,gorilla:0.008825):0.0096,orang:0.01831);\n+\n+The numbers are the branch lengths.\n+\n+**Beta: Within-species mode**\n+\n+You can also run Cactus in `pangenome\n+mode <https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/pangenome.md>`__\n+to align genomes of multiple individuals from the **same species**. In\n+this mode you will not use a guide tree. Cactus will use\n+`minigraph <https://github.com/lh3/minigraph>`__ to generate a graph of\n+the input genomes and then use the graph to order the alignments. To use\n+pangenome mode, select \xe2\x80\x98Within-species\xe2\x80\x99 in the \xe2\x80\x98Alignment mode\xe2\x80\x99\n+dropdown.\n+\n+\xe2\x9a\xa0\xef\xb8\x8f To use pangenome mode, you will have to remove spaces from the headers in your FASTA file.\n+You can do this with the NormalizeFasta tool.\n+\n+**Input**\n+\n+The developers recommend soft-masking your genomes with RepeatMasker\n+before running Cactus. RepeatMasker is available on Galaxy.\n+\n+If you\xe2\x80\x99re using Between-species mode, you need to provide labels for the\n+fasta files that match the leaves on the guide tree. In the example\n+above, you would use the label \xe2\x80\x98human\xe2\x80\x99 for the human fasta file.\n+\n+**Output**\n+\n+The main output of Cactus is in `HAL\n+format <https://github.com/ComparativeGenomicsToolkit/cactus#using-the-output>`__.\n+You can use the `Cactus: export <root?tool_id=cactus_export>`__ tool to\n+convert the Cactus output to a VG or Multiple Alignment Format (MAF)\n+file.\n+\n+\n+ ]]></help>\n+ <expand macro="citations"/>\n+</tool>\n'

diff -r 000000000000 -r 85f68b344286 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon Apr 04 06:27:44 2022 +0000

@@ -0,0 +1,25 @@
+<macros>
+    <token name="@TOOL_VERSION@">2.0.5</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">20.09</token>
+    <token name="@DIGEST@">c227e8d8aa41739667f54edbf19902d872dd07cba4c5046d613fe4ba2eb12a0d</token>
+    <xml name="requirements">
+        <requirements>
+            
+            
+            <container type="docker">quay.io/comparative-genomics-toolkit/cactus@sha256:@DIGEST@</container>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">
+                https://doi.org/10.1038/s41586-020-2871-y
+            </citation>
+        </citations>
+    </xml>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">cactus</xref>
+        </xrefs>
+    </xml>
+</macros>

diff -r 000000000000 -r 85f68b344286 test-data/bh1.fasta.gz

Binary file test-data/bh1.fasta.gz has changed

diff -r 000000000000 -r 85f68b344286 test-data/bh2.fasta.gz

Binary file test-data/bh2.fasta.gz has changed

diff -r 000000000000 -r 85f68b344286 test-data/evolverMammals.hal

Binary file test-data/evolverMammals.hal has changed

diff -r 000000000000 -r 85f68b344286 test-data/evolverMammals.maf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/evolverMammals.maf Mon Apr 04 06:27:44 2022 +0000

b'@@ -0,0 +1,238809 @@\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 000000000000 -r 85f68b344286 test-data/evolverMammals_both.maf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/evolverMammals_both.maf Mon Apr 04 06:27:44 2022 +0000

diff -r 000000000000 -r 85f68b344286 test-data/evolverMammals_noroot.hal

Binary file test-data/evolverMammals_noroot.hal has changed

diff -r 000000000000 -r 85f68b344286 test-data/evolverMammals_noroot.maf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/evolverMammals_noroot.maf Mon Apr 04 06:27:44 2022 +0000

diff -r 000000000000 -r 85f68b344286 test-data/germ_25.fasta.gz

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

diff -r 000000000000 -r 85f68b344286 test-data/hal2maf.maf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hal2maf.maf Mon Apr 04 06:27:44 2022 +0000

b'@@ -0,0 +1,30423 @@\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 000000000000 -r 85f68b344286 test-data/pens_25.fasta.gz

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

diff -r 000000000000 -r 85f68b344286 test-data/set_reference.maf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/set_reference.maf Mon Apr 04 06:27:44 2022 +0000

b'@@ -0,0 +1,2551 @@\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 000000000000 -r 85f68b344286 test-data/simCow_chr6.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/simCow_chr6.fasta Mon Apr 04 06:27:44 2022 +0000

b'@@ -0,0 +1,12054 @@\n+>simCow.chr6\n+TCTTTCTGGTGCGCGACCCAATCTGTAGACGGACTTAAGCTGAGCACACC\n+TTATGTGATTATATCAAGCAGATAGTCTTGCATTGATTGTGCAATGACTC\n+TATCCAAGAGTCAAAGACCAGAGGACTACGGCATAGTTTATTGGAATCCT\n+GGAGTATGGGTCCCCTAGACTCAGCAAAGCACTGGTTCCAAATGCATAGC\n+AGATAGTACTACAGCCTGGTGCTCCTGACTGCGAAATTCCTGAATGACGA\n+TGTGCTCTTCAGGCTCTATACAGTCATTCCATTGGGGAACTTAGGGTAAC\n+TGACGAACCTACACATTGTTTTTAACTATGTATAAAGTTCAGATAGTGCA\n+CATTCCCCTGTAATATGAATCAGTATATAATGTTGCCACTGCCCTAGTAA\n+CATGTATTTTGATAAGGTAACTGATCAGCTGAAGTTGCCAGAACACATAA\n+GGCAGCCCTAAGACAGATTGAGCTTCAGATATGGCCCACAAAGGCATTCC\n+CCTGCCTGATCTGGTCATATTTTGCATATTTTGCAATTACACTAGTCTGC\n+TTTATTTAGGTTAATGGAGCTTGATGAATGCATCAAAATAATAGAGCCTC\n+ATAAACACTTCCCACATTGCTCATTGTACAGAAGTTTACTTATATTAATA\n+TGTACACCCATCAGTGGTCATCTATCCAAAGCTCGTACAACAGAATACAC\n+ACAAAGCCTCCTGCCTCTGAGCACCATTATGCAGGTAATTAAGTGCAGAG\n+TAGGGCCATGCGATGAGGAAGGGTCAGTACCTGCTTTTCAGCTTGAGTGT\n+GGTGTAGGCTTGGGTAATGTCCTAGCGACAAATTACAAAACACAAGGACA\n+AGTACAGATGGGGATTTTTATCATTTTCATATTGTTACATGTTTCTGTGT\n+ATTTACTGCCCTTAATCAGATATAACCAATGACTTTCCTTCACTTTGGAC\n+TATTGCTTTTTATATTATATTCTATTCTATCCAGCAGGGCACATCACCTT\n+TCAAGAAATCTTCTGTCTCAGTTTGCACTAGGTAAGATACCTATGCTATG\n+GTTAGGAACATGTCTTGGTGAGATATTTGTGCTATGGTCAGGAACACTTG\n+TTGGTGATTACAATCAGATTGGATCCCATATTGCTTGTTTAGTCTCAAGA\n+TGCGACATAAAGGACTGCCAGGTTGTATGACTGTTAAGTCTTGGTGAGAT\n+ATTTGTGCTATGGTCAGGAACACTTGTTGGTGATTACAATCAGATTGGAT\n+CCCATATTGCTTGTTTAGTCTCAAGATGCAACATAAAGGACTGCCAGGTT\n+GTATGACTGCTAAGTTGTCAGTGGCTGTCTGGTTGCGAGTGCTGGGGGGT\n+TAACTGTATTAATATGCAGTGAGAAGGCCATTCTATCTATCCTGACTCCT\n+TATGTGAGCTTAAAGTTGTCAGGATAAAATCACCTCAGTGATCTCAAGGT\n+TTGTTCGGTTATTTCACCCCCTCTCCCAAGTCCTCCCCATGGCTACTACC\n+TTCTTAGTCCTAACTGATACATCGTAGTTAGATTTGTCAAGCGTACATTT\n+CCTGTCCCATATAGAGACTGCTCCTCTAGGAAGAAGACTCTAATCACCTT\n+ATGTATATCCGTCTTTGACTTGATCCACGTGTTATTTACACATTTAGCTG\n+CCCCTGCATCCTCTATATTAACCTGATTACATTTTGAGATATTAATTTGT\n+TTCTAAGAAACAAGCAAGATTGAATTACTATCTGTTAGCGGTACACCCAC\n+AGACTGTACTAAATTCATAGTAGCTCATGACCAAGTGTAGTCTTGTCAAT\n+GAATTATGATCAAATGACTACTTTGAAAGGGTTAGATCTGGTGGAATTGA\n+GCTTAGGTACTCCTAGACACTTGTGGTTATAATTTCCATCCCTCCTTACC\n+CTAGACCCATCCCATGTTGAAGTTCAAGGTTAAACATTATTCCTGTTGTG\n+TGAACTTTACcattaggtggggacaaccagctacacctagataggctagc\n+cgcccattgggaagattgtcttcaattaactacacccaaatatcccagag\n+gggagacatgagctctaaaatcattctaggacacatcaatacatcaccaa\n+ttgctgggtgacaatttggacacaatcatttgtattagattcctaatcct\n+agcatggtgttccttgttgggaggggtgaggacAAAAGTCACAGAACTGT\n+ATAACTTTTTGAGGAAAACAAACTTGTAAATGGATACGGTAAAACCAGAC\n+TTTTGGGCGGTATTTAGGGGTATCACCACTCTTTCTAAGTTACCTTTTTA\n+GGCCCAACTGAGAGGTTCAATTGCCCCATGGTTGTCTAAATTAGCTGCTA\n+TGCCTGTAGAGACCAGACTAGATTGCAGTTATTCTGCTTATGGGTCACAG\n+GCCATAAATTAGTGATCCTTCACTTGTTTTGCTGATGTAGCCTGACCTAT\n+CAGGCAATGTGATCTGTGAAATCCATGGGGCCTGTACTAGAAGGCTATCA\n+ACAGATGCTTAGGAATACTGGTGGGGTGTTTATGAGGCAGATGGGGAGGC\n+CATAAATTAGTGATCCTTCACTTGTTTTGCTGATGTAGCCTGACCCATCA\n+GGCAATGTGATCTGTGAAATCCATGGGGCCTGTACTAGAAGGCTATCAAC\n+AGATGCTTAGGAATACTGGTGGGGTGTTTATGAGGCAGATGGGGAGGAAT\n+TACCATATACAACAATGTGTGGTCCCCGTCAGCCTAACAATTCATGCTAA\n+TTGGAGGTTGGAATTATAGCTTGGTTGCTACAAATATGGTAAGGTGGAAG\n+TTATTTCTGTCAGTCTCAGTTTGCAGACTGCCACCTTTGATTGAGTCTCA\n+TTTTGAGGAATTTCACCTTTGATTAAGTCCCGGTAATACTACTAATTAAC\n+TTTTTTTATGCATACCTAATTGTCCACCCTCAATGTGGCAGTCAAGAATA\n+CCAGGACACTTGAAAATTTCATGCAGCTTCCTTTCTCACACTGAGGACTG\n+GAAGGCACACCATTAGGCAAAAAGATACCCTAATGCCATCTTAATAATAC\n+TAACAGCTATTGTTAATTAAGAGAGCGATATCCATCTAATCCTGTACAGA\n+CTAACAACTAAAATACTCAATAATTAGTGCGATACAATTCTTTACACTTT\n+AAGTGCATGAAGATCACCTTCAGCTCACAAAGAACTGGTGGTACCTTTCA\n+ACAACCCCAAAAGGAGACAACTTTCTGGTGACCCTGAGAGAAGACAACAA\n+GTGTTTTAGACGTTTGGACACAGTCAAACAGACTAGGTTAGTGGAGATCA\n+TTTCTTCCCATGACTGCTACACAATTCCAAATTTATAGCAATAGCCCATT\n+CTGAAGCAGAAGACTACCTAAACTCTGCACTTTATTGTGGGCATGGAGTT\n+ATTTTATATATATGTAAGCAGACCTTAAATGCCTGGCGTCATAGTAGTCA\n+ACCTCCTGATCTTTTGAGTGAATGCCCAAGTATAGCTGACTTGGGCATGC\n+TAAGTTATTTCTGTACTCTTCACTAGAATATTGACAGGTATAACAGTTGT\n+GTTGTCCTTTTATCTTTGCCCCCTCACTTCTAATTCCCTATCAAGGATTG\n+ATGAGTACTACTAAACAACACATTTTAGTGTTAAAGTTATCCCAAAACAC\n+CCCTTCAATGAACTGGTAAACCCAGATAGTGTGTGCCCTGAGTTATTAGG\n+TGTGTTCCTCCCTCAAATCCACTGGTGCCTGCTGCTATGGCCTCACTCCT\n+ATGTAAGGCAAAGAGACTAAGCTCCATTTCCTCATGAAGTATCTGTGGAA\n+GTCCCTATGCCT'..b'TTATAAGATAATTTACACTTTTTAT\n+ATTCTATTACCCAATCATAAAAATGAACATTAATGTTGCTTGATTGTTAA\n+TGGAAGATTGCTCTTGATTTTACTGTTTAACAATTCTTACAAGATGACAA\n+GATAAACTGGATGAACCTTGTGGAAGTAGTTTGAAAGGGCATTAGAATTG\n+TAATGATAGTACCGACAGCGGAAAAAATCATAAACTAGTTGGCTTCTGTA\n+TCATTCTTCTCGTTCAGTTATAAAGAGGTGATACAACTCTAGGAGTTTGA\n+CAGGCAGTGCCTGCTGCTATCTCTCATGGTCTAGGTGGTCGATATGAAAG\n+GTGCCAAGATGGACCAGCTATGAAGTATTTAGTATAAAAAGTCCTTTATT\n+GTATAAAGCAATGGTAACACTAATGGCAAAGTGTACCGCAGTAATGCTGT\n+TAGTTAGGTTATATACAACAGCTTCTTCCATAAAACATTGGGGTAAAGAG\n+GAAACCAGATTATTAATTCTCAGTTTAAAGCTTGTATTAGTGTTAAGCTT\n+GCTTGTCAAACACAAGCAATAGCCTGAACTATCTATCACATGGCAGAAGG\n+CCAAGATTATGGCTTTGTAACCTTCTGGCAATAGTCTAATCTCGCCTATG\n+TAAGGGCATACCATGGGGAGGTTCAGAAGGCACAAACTTTTTTTGGCTAA\n+GTGCGAAGCAAAACACCACAACAAACATCAAAATAATAAGTGTTACAAGT\n+GCTTTTAAGAAGTTGGATACTCTTAGAGTGTTTCTATTAAGACCCCTTTA\n+ATGGCCATCTAGACAAAGACCTTCGTTTGAAACACTGGCTGTGTCGTCAT\n+TCGTCACTCCCAACCCACCTTTTTCCTACTGGAGATATGATAAGAGTGCA\n+TTAAATTTAGTGCTGCTAACCAGGTTTCCAACAGATGTCACATTCCGGTA\n+ACTTCTACATTGCGTGTTGCTTTCCAGTCTATATCTTACTCGGTCGGCTA\n+TGAACATCACCCCCTACTATATATCAGGTCAGGAGAAAGAATCTACAACT\n+ACATGCCCATAGAAGCAGGCCCCATATTAATTTGGACTTATTAGTATTGC\n+CCAAAGTAGTTTGTACTTGAAATTCAGTATAGGTCATCAAGGAACAATGG\n+ACTGGTCTCCCTAAGGGACTAAACTTGGCTGGATAGATGTAAACTACCAA\n+TAAACGGACCCTACCCCATTAGACCTTCCATAGAAGATAAATCATTTGGA\n+GCTCACAACAACTCAGAGTGTGTTTGTTAGTGGTGTGTATTAATCTACTT\n+TAGAAGAACACAGGTGATCCGATGATTAGCGCAATTCACAGGATTCACAt\n+ccagtgtcattctagaacaggccgatagacataatttatttggcattgta\n+ggtcccactcaactgatcctggtttcaactaatcctgctaatcctggggt\n+gaaattcaactaataactgggtgaaacagattttgaataatatcatttct\n+tagcatggtatttctcgtagggaggggagaggattaagttctaaaatttT\n+TTCACCCTTTACCAAGCCACTATCTTGGAGGAGCTCAGTCTTTTGGGCTA\n+AGTCAATTCCATTCACCTATACGATTGCACACATGCATTATACTACACCT\n+GGATCCAGATAAAATTGGCTATCCAGATAAAATTGGCTGGGTTGAGTCAC\n+ATGCAATCCCTTATACATGTGCATTTCACACACTTGAAATTCACAGAACT\n+AACTGGGAGTAAATCCTACTACTGGCAGCGACCCGAGACCTTATAACAAG\n+TCTTTCACTCCCTGCACTTTTGGTGATGTACACTTGATATATTTCTACTC\n+AATGTCACTGGGACACAACCCCACCTATAGATTGTTTAAACAATGCTGGT\n+TCAACTATTACCAAGGCACACACCGACGTGCCCTTGCCCTAGGAGCTGGA\n+GAAATTGACAGGTTACCTCCAGATGACGTTAAGTCTTTGCAATAAGTGCA\n+AAGTTACACTCAAAGTCGTTGTCTGCTGGGTTAGTACCTTCTGAAATAAT\n+TACAACTCTCAGATGTACTGGTGAGACTTCCTGGCATTCCATGGCCCTCC\n+CCCCTGAGGTGGACTGGAAAGAGCACTTGACCAAAGTGGCTAAATAGCCT\n+GTTGAATACACTGCTTTGCCCTATCAGCTAACAGAACAGATAGCTGCTCT\n+CCAAAGCCATGGAGTATTAGCCACATATTGAAGCTGAGTACTAGGACCGC\n+CACCCAACTAGCTATAACCAACCTCTACAACTGGCCAGTGTAGTCCAATA\n+TACCAGTTGCAGATTTACATAGTACTGACCCCTGCAAGTTAGGTGGGGGT\n+AACCAATCAGGGGATCATTTGCATCCAACCTCAACATGGTAGCCTTTCTA\n+ATTTACAGGTGGGTTGAATGAGCAACATTGATCTGCCAAGAACAACCAGT\n+ATATACTTCTAATACTGCAGAATAGATCTTTACAACAAGAATTCAAAACA\n+TATACTAACAGATGAGAATTGTTGCTAATCCATTCGATGTACTGCACTAG\n+CAATCCAGCCACAAAGGCTTCAGAATTAGAGGAAGGTATTATAAGACTTT\n+TTTATAAGATTTAGATACAACCCTGTTTGAACAATGAACTTGGGTTTTCA\n+AAGACTTGCATTTTCATCAGAGATATGTGTGTATCTTTTCTAGCCAACTT\n+AATAGCTAGCTGATCTTTGCAACCTCTGAGTGTTGGCCACACCATTGCAC\n+GATAAGTACCCAGCTATTGGTGACCAACCTGTGGAACTGGCCCAAGTACT\n+TCATATTTATCAGTTGAAAGTTCACATAGTACTGACTTCTGCAAATTTGG\n+TGGGAGTAACCGATATGGGGGTCCTTTGCATCCAATCTCAACATGGCCTT\n+CCTTCTATTTTACAGGGGGGATGAATGATCCACACAAGTGGACCAAGAAC\n+AATTGGTATGGACTCCTAATACTGTAAAATAGATATTTACAAGAGGAATT\n+CAATACACAGTCTGAGTCTGGAAGATGAGAATTGTAGACAATCCAGTCTA\n+TATACTGCGCTAGCAAGCCAGTCACAGAGACTGGAAACCCAAAAAGGTAT\n+CATAAGATTTATTCATTAGATCTAGTTAACTCAGGACCTTTTCAAAAGCT\n+TGCATTCATCAGAAATATGTGCGTGTCATTTCTAAGTTTTAAATACTTTC\n+CTGTTAAGCAAATAGTTGTAAGTTATTGCATGTTTAATGTGTTACAACTT\n+ATTTTAGTTCACCAGGTGCCAGAGTTCCATTTGATGACCTGAGAGGGTGG\n+GAACAATATTTTTTTTATTCCATCCCACAAGTAGTGGCGAGTTATCTGAC\n+ATTTGTGGGAACAATCTTTTTTTTATTCCATCTCGCAAGTAGTGGGAAGT\n+TTTCTGTCCTTGATATCTGCCAATAGCTTGAAATGGTTTGTTCAAACTGC\n+AAGCTCACCTGAGACATGAGGAGTCTGGGTAGTTTAGTAACCATTGTGAT\n+GACAGATAAGAAGCCAAAGTTTAGAAGCCAAAAATTTACAACTACATTGA\n+ACACAAGGAGCGAGGCTATAAGCAGGCCACCGAAGATGAGACATACACTT\n+CCCTAAATGAGTGCCTTGAGTTCCAAGAGGTATGACCACCTTGCTGACCC\n+TAGTATGATAATATGACATTTGTCAGTATAATGCCTGCGCACCAACTTTT\n+GTGTCAGAGACCATGAAACCAACTGCTCTGGAAGATAGCAGTCTCATTTG\n+GAACAGTGCCAAAGATCTCAAGAACTGTTGTTGCCCCTGTTATATTTATG\n+AGCAAACCCTCACCCCAGCAAATGCTTTGTGTGCTGAGACTCACTCATTG\n+AAGACACTGTTATGAAAAT\n'

diff -r 000000000000 -r 85f68b344286 test-data/simDog_chr6.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/simDog_chr6.fasta Mon Apr 04 06:27:44 2022 +0000

b'@@ -0,0 +1,11879 @@\n+>simDog.chr6\n+TCTTCTCTGGTGCACTACCCAATCTGTAGACAGTCTCAGGATACAAACCT\n+TATGTGACTATATCAAGCACATGGTCTTGCATAGATTGTGCAATGACTCT\n+ATCCAAGAGTCAGAGGCTGGAGGACTTATTACATAGTTCTCTGAGAATCC\n+TGGAGTCTTTATCCTCTAGATGCCGCAAAGCGCTGCTCCCGAATGTACAC\n+CAGATGGTGCTACATCCAGGAGTACCTGATTTAGCAATTCCTGAATGATG\n+GCTTCTTCCTTAAGCTATTTACAATCATGACAGTGGGGAACTTAGGGAAG\n+CTGCTGAAGTAAGAAATTCCTTTTAACCAAGCATGCATGAAGTTCAGACA\n+GTGCACACTACCATGGTGATATGAACTAGCATATAATGTTGCCAGAGCCC\n+CTGTAACATTTATTTGATAAGGTAATTGGTAAACTAAAGTTGCTAGAACA\n+TGTAAGTATGAGACCTTACGCAGCCTTAAGGCAGTCTGAGCTTCGTATAC\n+AGCCCACAATTCAATGCATCAGCCTATCTGATCTGGGTAAGATGTGGGTA\n+CACCCTGCAACTCTACTAGTCTGCTCTGGGTTGGTTGATGAAGATCTACA\n+GCGGCATTAAAACAATAGAGGCTCATAAACAGTATTGTGCAGAAGGTTAA\n+TTATTGTGATTTCAATTATGTCCACCCATCAGTGGTCCTCTATCAAAAGC\n+TGGCACAACAGCATACAGTCAATCATTTGCGCTGGCAACAAGAATAGCCA\n+GTACCTTATTTTAGCATGGTTTTTGTCTATTTACTGGCCTTAAGCAGATA\n+TACCTAAAGACTTTGCTTCACTGTGGATATCAAGTCTATACTATCCAGCA\n+TAGCACATCACCTTTCAAGAAATCTTCTGTCTCTGTTAGCACCAAGTATG\n+ATACTCATGGTATGGTCAGGAATATTGTGGTGATTGCGATTaggttggat\n+tccttattgctcattcagtaatcaggatgcaatatagctcaagagtccca\n+ggttttttgactctccggtcgAGTGCCGGAAGGTTAGTTGAATTAAAGAT\n+GCAGTAAAGAGGCCACCCCTACCTCATGCACCTTATCTCCCTTATGGGAG\n+CCTAAAGTTGTCAGGATAAAATCCGACAGGTAATCTCAAGCTCTGTTCTG\n+TTATCTTTCCCCCTCTTCCAAGTCCTCTTCTCAAATAATACCTTCTTGAT\n+ACCAATTGGTATATCATATTTAGATTTGTTGGGTGTGCATTTGCAGAGGA\n+ACATGTTACCAACGTGGCCATCTTATGGCTGCTGCCAGTTAGGGACTCCT\n+CCTCCATGAAGAAGACTCACCATATGCATATTCCGTTTTGGCTCTTGTTA\n+TGCTGGATTCTGAGTGGAGTTTCTACGTTTAGCTGTCCTTGCACCCCTTA\n+TACCAACTTGACTACGGGTTCGAGATTTTAACACTGCTCCTAACAACTAA\n+GCCAACTGAACTGCTAGCTGAGGAGTTGTGTCACTCCTGCTGGCTGGATT\n+CTGAGAGTAGTTTCTACATTTAGCTGTCCTAGCCCCATTTGTACTGACTT\n+GATTACGTTTTGAGATTAATGCTGCTCATAACAACTAAGCAAATTGAACT\n+ACTAGGTGAGGAGTTGCATTACTCCGACAGACTGTATTAATTTAACAGTA\n+GTTCATAACCCGACATACTCCCATCAATGAATTATGATTGAATCGCTTTC\n+TCGAAAAGGCTAGATTTGTGAGAAGTCAGATATTCACCCTGGTAGCTGGA\n+TACTCCCCCTAGACACTTTTGCACTCTTTCTCCCCCGAGCCCTGGCCCAT\n+GTTCGGGTTGAGAGTTAAACATTACCCCTGCTGTGTGAACTGTAACATTC\n+GTGgggctccaacattgttctggaacagctggatacacctagttggcttc\n+acctcgttagtcccattcaactaatccaggggtgaaaaaaattttggaca\n+caatcatttgtattaggatcctaatcctgacacggtattcctgttgggag\n+aggagaggactcagttccaaaCATTTACAACACTTTGCTGCTTCCCGAAG\n+AAGCATATAAAATTATATGTGAATATGGTAAAACCACACTTCTGGGAGTA\n+CTTATGCTCATCACCATTCTTGCTAAGTTACCCTTTTTGACCCAACTGAG\n+GTGTTCAGTTAGCCTAAGGTTGACTAAGATAGCAGGTCTATGCCTGTACC\n+GACTAATGTAGGCTGCAATGATCTCTTCCATGGGTCACGGTCCATAAATT\n+AGTGACCCACTTACTTATTTGCTGTTGCACCCTGACCTATCAAGAGCAAT\n+CTGTAAGGTCAATCTTTGAAATGCATACTTACCTATAGGTGTGTAGAAGC\n+CACACTAAAGGAGTGTATGTGAGCTAGATGTGGAAGAATAACATTTATAA\n+GAGATTGGTATGGTCCACTTTGGCACATTTGGTCCAAATTGGAGGTTGCT\n+ATTATAACTTGCTTGCTGAAGGTGTTAGGTAAAGTGTAATTTGTTTCTGT\n+CAATTTGCAGAATGCCACCTTTGATTAAGTGTCTTCTTCAGGAATACCAC\n+CTTTGATTAAGTCCCTCTGATACCTCTAATAAGCTTTGCCTATGCAGAGC\n+TGATTGTCCATCCTCAATCAGGAGATATGGCTGCCAGGGGTACCGTACAA\n+GACGCCTCATAAGCACAACCTAACTGGGGATCACCATTGACCTGTAGTGT\n+CTACAAAAGGCAAATGCCATTTTTATAAGCTAACACATATCCATAACTTC\n+AAGAATGATATGTATCTACTCCTGTACAGACTAAAAATCTAAATGATATA\n+ACTAAATAATTAGTGGTGATAAGGTTTCTTCATACAAAAACACATTAAGC\n+TCATGAAGACCATCTCTATCATACTGATGGTATATCTTTCTTGTGAAACC\n+CTAAAGCGAGACAACAAGTGGTGAAGAAAGCTTGCATACAAAAGTGCACG\n+AGGTTAGTGGAGATCATTTCTTCCAAGAATGGGAAATCAATTCCAAACTT\n+ATAGCCCATCCTGAGGCAGAAAACAACCCAGACTCTGCACTTTGTTGTGG\n+GCACAGAGTTAATCTATATATTGTCTAAGCAGACCTTAAATGCCTAGCAT\n+CATTGGAGTCAACTATCCAATCTTCTGAACCTCAGATTACAGCTGATTCG\n+AGTGAACTATGATATTTCATAACCTCTTCAGTGGACATTGGTACAGCATG\n+TATGGTAGTTGTGACGTCCTTTTATCTTTGCTCACTCACTTCCCATTCAC\n+TTTTAATGATCCATGGGTATTACTAGAGACCTTTTTTGTGTGAAGACTAT\n+TGCAAGATACTCTAACCGGAACCAAAATCTTGCGTGCCCTGTGTAATTAA\n+GTGTGCTCTTTTTCTAAATATGAAGGGGTTCTTGCTGCCATGGCCCCACT\n+GCTCTGCATGGTGACTAGACTAAGGTCCATTTCGTCATGAAGCATCTGTC\n+GAATATCTTATGTATAAGCTTGTCCTTCTGTAGTGAGATTCCTCCACAAC\n+ACCAGTACACCATTGATCATGTTAAGGCTTTTCACACGTTGACAATAGAC\n+AGGCTGCAAGGCTATTCAACAGGTTTAAATCAATGAGGGAGAGAAGAAAC\n+GTGGCTGGTACAACCAATCTGACAATTAGGTTAAGAAAAGACTACTGTAG\n+CTCACTACAACAACTGCTGGTCCTAAGAGGGCAATAAGGACAGACAGAAA\n+CAATAGTCCATTGCTTGATTGGTTTATGCCACTACAAGCCTGAAGTGATG\n+TTTTGAAACAGAGTACATGAACATGGAAATGTAAGTCCTATGCAATAAAA\n+AGGGGCATTTAT'..b'AAAATTGGACCCTGGTCATCACGTCGTCCGGGTGGCTATAATTTTTCTC\n+TAGACATGCTCATCTCCCTCGTTAGCTTACACAGCCTGTGAGCCGAGCTG\n+GACTTTCTTATACCTAATCCATAGTGAATTATTCCTGCCTTTTGCACACC\n+AGGGTTGACCTTCCCCAAGGGTCGTTTTGTTATGTCATCTGCAATGGACT\n+GAAGAATCTTACCAGTTGTGAGTGATTGATGATTTTAATATTGGCCATAG\n+GTTCCAAAAAAGATTCCCCCTCAAAACAACTAGCACTACATCAGAAGTAC\n+ACTAACAAGTGGAGCCCAGAGGCTAGCTTACAAAATATTCACGTGACACT\n+AAGCTCTGGCACATAAAAAAAAGCCCTTCTTGTTCATGTTACCCGATCCA\n+GTTGTTATAACCTATCTTAGATACCACTGAATCCCAAAAACGAATATCAA\n+TGATGCTTTCGCCTTTAAGGGCAGGTTGCCTTTGATCTAAGGGTTCAATG\n+CCTATAAGATGCCAGGATAAATGTGGATGAAACTTGGAGAAGCTGTTGAA\n+AAAGGCATAGAAGGTCTAAGGATAGGATGATAGGGGGAAAGATCATAAAC\n+TAGTTGGATTTCATTTCAGTTTTCTAATTCAGTTATTTAGATGAGATATA\n+ACCCTAGGAGCCTCATCAACCTTGTGACTAACGTTGAACTGCCACCtccc\n+aattttatgactttcaggtcatgagcactgggtggttaataTAAAAGCAG\n+CTAAGATGGACCATAAGTCATTTAGTATTAGAACTCGTTTAGTCCATAAA\n+GTAATGACAATGCCAAGAATTAAGTGTATGGCGGTAATTCTATCAGTTAG\n+CGTGTATACAGAGCTTCTCATGATATATCAGCCAGTAGGAAAAAAGTTTA\n+TAGATTGTTATTCTGTATTAGTTCGTAAAGACAGTAAGCTTGCTTGTCAA\n+ATTCAACAGGTATAATCTAGACTATCTAACTATAGGTCTTAGATAGTGCG\n+TTTTGACCCTCTGGCAATAGTCCAACTTAACCCATGTGTGGGCATGTGTG\n+GGGGTAGGTTCAGAGAAGGGACAAACTCTACTTGAGTAAGTGTGCAAGAC\n+ACCACAACAAATGTCACAAGAGATTAGTGTTATGAGTGCTTTTAAGAGGT\n+TGGATACTCTTAGAGTTCCTTTACTGAGACCCCATTACAGGCCATTTAGC\n+CAATTTGAAACGCTACCTGCCTTGTCCTTCTTGTTACCTCCTAACCTTCT\n+TTCTACTGGAGATATGGTTATGGTCAGTGTGCATCATATTTAATGCTGCT\n+GACAGGTTTCTGTCAGATGTCACAATCCAGTATCTTGTATGTTGGGCAAT\n+GCTCACCAGTTCATCTCTTCTTAAGTCAACTACCAAACATCTCCATGTGC\n+AGCAGCACCAGGCCCCATATTAACTTAGATTTATTGGTACTGCTTGCTGC\n+CCAAAGTAGATTGTGTATGAAATGTAGTAGTGTAGGTTACCAAGGAATGA\n+TGGACTGTTCACCCCCAAAGAACCAATCTGTGATAGCTGGATAGATGTAC\n+ATAAAGCAAATGGCAAAATTGTCTGACAGAATACCAGATCATGCATGATA\n+ATGAAACAGGAATCTCATAGGAATGTTCTGCTTCAAGGCATATGACCCAA\n+TTGGTCTTCCTGGACATTCCAGTCCTTCAACCTAATATGATGAGTCATAT\n+GAAAGGCCTTACTGCATGAAGCCTTCCTTTGGAGATAAATTGTAGGGAGT\n+TAGTGATGACTACAAGCATCTTTGCTAATGGTGTATATTAAACTGCTTTA\n+GGAGGACGGACACAAATGATAGTTCCCACAGAAATCATAtccaacatcat\n+tctagagcaggctgacatggctagtcgactttgcagcatcggtcccacaa\n+tcccagggtgaaacgacaaatcccggggtgtaaaagattgtggacacaat\n+cgtttgtattaaaatactaccagtatacccttttgggagaggagaggagt\n+caattctaaattctCCCCCTTCACCAAGCTAGAGGAGGTCAGCCTCCTGG\n+GCTGATTCATTTCCATTTACCCATTCACTTGCATTCACACTCGCATTATT\n+CCACCCGTGGATTTAGATAAAATTGGCTGGGTTGATCCAGTTCCACTCCC\n+CTAGACACTAGCATTTCCCACACTTGGAATTTGCAGGGTCAACTAGGAGT\n+AGATTTCAGGGCACTCCTTGCAGGGACCAGAGGCATCATAACAAGTCTAC\n+CCACAGATGGTTTACACACTGCAGGTTCAACAAATGCAGGGGTGACCACT\n+TCTCACCTTGCCCTTGGAGATGGAGAAACTGGCAAGTCACCTCTAGATAA\n+GGTTAGCACCTTGTCCATAAATCTTTACCACAAATGACCACTAGTCAGGG\n+CACCACTGGCAGGGACCAGAGACATTATAACAACTGCTTCAGTCTCTGCA\n+TTTTTGGTCATGTTCACCTGATATATTTTTTCTCGATGCCATCCAAAGTC\n+ACACTCAAAGTCATGTTTTTAGTTAGCACCTTCTGAAATAACCACCACTT\n+TCATGTGTACTGAAAAGACTTCCTGATATTCTATGCTCCTCCCCCCCAAT\n+ATGGTCTGTAGAGAGCACTGGACCAAGTAGGCTAAAAAGTCTCTTCGACA\n+GTTGGGGGGTGGATGTAATTTATGTGCACTCTGAGTCATGTGGGTTCACT\n+CTATCATCAGCTAACAGAATAGCTAGCCAATTTATGAAGCATCTCACTAT\n+TGGCCCTTGCATGCAAAGTACAGGAGACACCACCTCACCACCTAGCTAGC\n+AATGACTAACCTCTCACTGGCCCGGGTACTGGGTATGTACTCAAATCCAA\n+ATTATCAATTGCAGACTTACTTACTACTGACTTCTGCAAATTAGTTGAAG\n+GTTAACAATCTGGGGGTCCTTTGCATTCAATCTCATCATGGTCTCCCTCT\n+GATTTACTGGGGGGTTGAATTATTTTGACCAAAAACAATCAAAATTTACT\n+TCCAATACTGTAGGAGAGATTGTGAGTGGATACCCAGGTCTTTACAGCAA\n+TAATTCAAGACACTGTCTGAATTTCGACAGATAGTTTTGACAGATGAGAA\n+TTGTTGCTAATCATTTCCATATAATGTGCTAACCATCCAGTCACAAAGAT\n+CTGAAAATGGGAAGAAGGTATTGAAAGATGTATCTGTAAGCCCCAGATAA\n+ATCACAACCCTGTTTGAAAGACAAGGTCAGCCCTTCTAAGACTTGCATTT\n+TGATCAGACATCTGTGTGTATCATTACTAAGTCTCTTAGAATCTTTCCTG\n+TTCAGCAAGCAGTTGTAATTTTGTTATTGTTATCTTTAAGGAGTTACGAA\n+CTACCTTAGTCCTGTCAGAGTGCGACTTCATCACACTGAGAGGGTGTGAA\n+CAATCTTTTTTTTATTTGGTGTCACAAGTGCACAGGGGAGTTATCTGCTA\n+GAAGCCTCACAGGGAATTATCTGTCTCTGACACCTGCCAGCAGCTTGAAA\n+TGGTTTATTCAAACTGCACCCTTACCAGAGTCCCGCGTAGTCTGTGGGTA\n+GTTTAGTAGCCATTGTGACAACAGAAGCAAAAATTTAGAGGCCAAAAATT\n+TACAACTACACTAAATATAGTATTCAAGTGAGAAGGAGGAAAACTAACAT\n+CCTAGAAGTGGAGCATTAACTTTTGTGCCAGAGACCATGGAATCAACTGC\n+CCGGGAAGACCATCAGCTTGTATTGATGTTGCCACCAAAATTCATAAGAA\n+CTGTTGTTCTCCATGTTAGATTCAAGAGCTCACTCTCACCCCAGCACATA\n+CTTTGTGTATATTGAGACCAACACATTGAAGACACTGCTATGAGAAT\n'

diff -r 000000000000 -r 85f68b344286 test-data/simHuman_chr6.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/simHuman_chr6.fasta Mon Apr 04 06:27:44 2022 +0000

b'@@ -0,0 +1,12039 @@\n+>simHuman.chr6\n+TCTTTCTGGTGCAATAGCCAATCTGCAAACAGTTTCAAGATGAGCACACC\n+TTATATGACTATCAAGCATACAGTCTTGCCTAGCACACAATCTTGCATTA\n+GATTGTACAATCTCTCGTTCTGGGAGTCAGAGACCAAAGTACCTACTGTG\n+TGGTTGATCGGGTATCCTGGAGTGTTGGTACTCTAGATTAAATAAAAATG\n+CACACCAGATGTTCCTACAGCCAGGTATACCTGATTGAGAACTTCCTGAA\n+TAATGGTGTGCTCAGGGAGCTCTATACAGTCTCTACATTGGGGAACTTGG\n+GAAAACTGTTGAACTTACAAATCACTTTTAACCAAGCATAAAGTACAGAT\n+AGTGCACGTTTCCCTTGGACATGAACAATGCTACCACTGCCCCACTAATA\n+TTTATGTGACTATAAGATAATTGATGAGCCGAAGTTGCTAGAACAATTAA\n+GTAAGAGCCCCTAAGCATCCTTAAAGCAGTGAGATATGACCTGCAATTCA\n+AGACAATCCACTTGCCTGATCTGGGTATATTTTGCAATGCTACAGATCTG\n+CTCTAGTTTGGAGAATTGAGTGCCACAGATGCATCAAATGCTTAGAGTCT\n+CATGAACACTACCCACATTGCTTATTGTACAGGTAGAAAATTGGTGACCA\n+GAACTACACCCACCCATCATTGGTACTCTTTCCAAGGCCTTAAaactaga\n+agagttaccactgaattagaagagtgatatgaaatctccagcttCAGTCA\n+AATCATCACAATAGCCCACTGCTGCTTCTGTCTCTGAGCACCATTCTACT\n+GGTAACAAAGCACAAAGTAGGGCCATGTGTATTTTGCACATGGAGTAGGT\n+AGGGTTAAGTAATGCCCTGATCGTAGGGTAACACAAGGACAATTACTCAT\n+GGGGATTCTCAATATAACCAAATTGTTATGTATTTTTGCCAATCTACTGG\n+CCTTAAGCAGATAGAACTAGAGGCTGTGTTTCACTTTGGGTATTGATTCC\n+ATACTATCCAGGGGAGCACATCACTTCAAGAAGTCCTTGAGGGTATGCCC\n+GTGCACCTTAGCCCAAGAATAGGCCAAGTTAAAACCGGTAGGATGCGGCG\n+CAAAACCCTGTCAAGAAATCTTTCGTTTCTGTGGCACAGAATGTGATACT\n+TCTGGTATGTTCCAGGGATACTTGATGGATTACAGGTAATTACAATCaag\n+ttggattccatatcacttgttcagctattaggtcacaatatagctcaagg\n+agtcccaggctttatgactctcaTGGTGTGTGTTGGGGGCTAGTAATATG\n+GATATTAAAATCCAGTAAAGAGACCTCCCCTACCCCATGAGTCTTGTCTA\n+CCTTTGTGAGCTTAAAGTTGTCAGGATGAAATCTCACAGGCCATCTCAAG\n+CTTTGTTTGGTTATTTTTCCCTCTTTTCCAATTTCTCCTCCTGAATATTA\n+TGTACTTAATACCATCTAACCATCTGATGTATCATATTTTGTTTTGTCAA\n+GTGTACCCTTGCTGGGGAACATGTTCCTGATATGGCCATTTCTTGGCTGC\n+TCGCATATAGAGACTTGCCCTCTACAAAAATGAGTCTAATCACCAGGTGC\n+AATCCCCCGTGTTTTTGACTCTTGTTGTGCCAAATCCTAGCATTGTTTGC\n+CCACTTAGCTACTAGCTTGACAACATTGGAGGTGTTCAGACTGTTCCTAA\n+TATCGAAGCAAACAACTAGGCAAGATTGAACTCACTTTACGAGCTGAGTA\n+GGCATTATTCTTCCACATTCTGTAAATGGAACAGTAAGTCTTTAACCTAA\n+TGAATCTAATTAGAGAACTACGATCAAATGACTATTTTGAAAGGGCTATA\n+AGGGGATTTGTTGATACTAAGATATGCCCCTATTCCTGATATGCGATCTG\n+TACTGACAGAACCGTATTATTCATCGAGCTAGTACTTATGGACCATATAG\n+TTTGAAAACCTGATGGAAACTTGTAAATGAATAAATATGGTAGAACCGAC\n+ATTTCAGAAAGGGGTAGGTCTTATCCTCATCACCATTCTTTCTAAGTCAC\n+CTCCATACACCAAACTGAGATGTTCTATTCTAAAGTTGTGTGCAGTAGCT\n+AAACTATGCGTGTGGGGGCTGAAGTAAACGGAGGTGACTCTATGGAAGGG\n+GTAGGTCTTATCCTCATCACCATTCTTTCTAAGTCACCTCCATACACCAA\n+ACTGAGCTGTTCAATTCTAAAGTTGTCTGCAGTAGCTAAACTATGCGTGT\n+GGGGACTGAAGTGACTTGTGGTGACTTTATGGAACATGGGCCAGAAGTTG\n+CTGACCCTCTTGTTTTTTTGCTCTTTCACCCTGACCTATCAAGCGAGGTG\n+ATCTGTGAAATTCAGGGGACGGGCCCTTGAAGTCTTTCTTGGAAAGGTAT\n+ACTTGTCAGGTATGCAGATTGTGGTTAGCCTTGCGCCAACAGTTGGTCCT\n+AATTGGAGTATATTATAGCTTGCTTGCTGAACATCCTAGGTAAAGTGTAA\n+CTTGCTTCTGGCAATTTGGGGAATGCCGCCTTTGTTTAAGTGTCTTTGGG\n+GAATGCCACCCTTAACTAAGTTCAGTCAGTGGGACCACCAATAAGCTTTA\n+CTTAGCCATAGCTGGATTTTCACCTTCACCAGGAGATAGCGATTGGGTGC\n+CAGCTACCAGCACACCTCATAACTTTATTTTGTGCAGCTTCCTGCCACCA\n+ACTGGGAACTGTAAGCCCCACTATTACCTGGTAGTGTCTACAAAAGGGAA\n+ATTTGGGTGCCACATAGCACTCCTGTTAGACTAACATCTGTTACTAATAC\n+AGAGAATGATATCTATCTAATCTTGTACAGGCTAAAAAGTAAAATGAGAT\n+AACTAGATAATTAGTGGTGATAAGATTTTTCCATACAGAACACACGAAGA\n+TCATCTGCTTATGAAGATCATTTCTATCATACTGATGGTATGTTTCTAAG\n+ACTAAGACCTATTATGCCTGTAGAGTATGATATCTGTCTAGCCTTGTACA\n+GAACAACTAGTGCTGGTGAAGTTTACACATATGAAAGCTTACTAGGTTAG\n+TGGGGATCATTTCCTCCTATGATGGCTGATCAATTCCAGGGGCTCACTCT\n+GAAGCAGAAGACTACCTAAGCTCTGCACATTATTGTGTGCACAGAGTTAT\n+TTGATGTATACATTAACCAGACCTTAAAATGCCTAGCACATAGTTAACCA\n+TCTAATCTTCCAAATCTCCAAGATCTGAGTGGGGCAGGGTATCTCATGAC\n+TTCTTCACTAGCCATAATACAATGCATATAGCAGTTGTGTTATCCTTTTA\n+TCTTCGACACACATAACAGTTGTGTTGTTGTCCTATTATCTAAGCACCCC\n+TCACTTCCAATTCCCTGTTAGTGTGATTTGTGGACATTATTGGACAACAT\n+TTTGTGTAAGTGTTATTCCAAAAGACCTAACTGGAGAACCCAAATATAAT\n+GTGCCCTGTGCAATTAAGTGTGCCAATCATAAGCTTGCCGCCATGTCTCC\n+ACTGCTATGCAAAGTGAATAGATTGAGTTTCATTTCCTCATGAAGAATCT\n+GTGGAACATCTTGTGTATAAATCGGTTTTCCTGCAGTGAGGTCCCTCTCA\n+CATTCCACACTCCTTGTTATCACATTTAATATCCTGGTGTAGTCTTCAAT\n+CTCCTAAGTACTATGTATTAAACAATCCTAATCTCAAAATTTTCTGTCTC\n+CTTGATGTATCAGCTCTATTTTTAAAAATATGACTGCTACTGATCTATGC\n+ATCTTGCAATGCATCCTGTCCAAAGGGTCTTCTGGTCCAATTTGTTCATG\n+GTGCATAAAA'..b'GTGGTTGGAACTCATCCAAAGCTATAGCGAT\n+ATAACGGTCGCCAATGCACCGCCCAGCTCTTAGCGATTGGCGACTGCCTT\n+CCCCAATGTGATACCCAGGTTGTTGGGTGCACTTACTGGACACCCGAGAA\n+AGCAGGTCTAGGTAACCAACTAGGGGCACCCTCACATGATCAGACCATTG\n+CCCCTCGACTCTTTAGTCATCTCGATCGGAGTTTTATCTTCACCCCTGGT\n+GTCATAGTATCAAGGGGTGTCTTCGGGACCTGGAGGAAGGGAATTATATC\n+GGATATTAGTGAAGGTCCGTCTGATAACTGGAGCCCGCTCATCAATCGTT\n+CAAGAGGCACCATTGTGTGTTCCCTGGGCGTACTCCTTTCCCACGTTAGC\n+TTACAGGGTGTGGAGGCTGCGCTTAATTATCTTATGCATTCCTAGTATTA\n+TTCCTACCTTTTTCTTACCAGGGTCCACCTTCCGCAATGGACTGAGCATC\n+CTAATAATTGTTAGTGATGGATTTTAATGCCGGCTAGAAATGCCAAAAAA\n+GCTCAACCCTCAGGAAAAATGGCACTACATCAGAAGTACTCTAACATAAG\n+AAGTCTAGAGACTGGTTTAAAAAATATCCATATGATTCTAAGATCTGCCA\n+AAAATTCTTCTCAATTGTGTTGCCCAACTCAGTTGTTATAGCAAAACTTA\n+TATTCTAATCACCTAATCCTAAAAATGAACATTATGGCAGTTAGGCCCTA\n+GTTTGCCTACTGAAAAAAAAGTCGTAACTAATAAGGTGAATCCACGATGA\n+TGTTGCTTTCACCTTTAAGGGTAGGTTGCTCTTGATTTGAGTCACCCTCA\n+TTCAACTTCCTATAAGACTCCAGTAAACCTTGTTAGGGATGATAGAAGGG\n+AAGATCATAAATGATTGGATGCCATATCACTAACCTAGTTTAATTGTTAA\n+GATGCAACACAGCTCTAGGAATCCCGCAGGCAATGTCAAGCTATCCCCTT\n+CCAGTTTTAATACTTTCAAGTCTTTCAGGCATGAGTACTGGGTAGTATAA\n+AAGCTGTTGAGATGGCTCCACCAAAAACCAAACAGTATAAAAACTTGTTT\n+AGTGTATAAAGCAATGGTGATGCTAATGTTTGGCAGTAATCCTATTGGTT\n+AGGGTTGTATACAACATACAACATCTGCCCATGGAAGATTGGGGAGGAGG\n+ACACCAGTCTATTGATTGCTTAGTTCATGTTAGTTTGTCTTGCCATTAAG\n+CTTGCTTGTCAGATCAAATAGCTTGCTTGTCAGATCAAATAGGTATAACC\n+TGGGCTGGACAAGTAATATAGGTTAGCTTGGGGGTTTTTTACCCTCTGAC\n+TACAGTATAACCCCGCCAATGTAAGGTTGTACCATGGTCAGATCCAACTG\n+GTGATTCGTAGAAGGCGCAAACCTAATCGGGCACTTGTGTAACATACAAG\n+AACAAACATCACAAATGATAGTTGTTATAAGCATTTTTTTAGAAGTTTAA\n+TAATCATAGAGTGTTTCTATTAAGACCCCATCGCAGGCCATCTATTAAAA\n+TACCTTAGTTTGAAACACTGGCTCTGATGACCTTCCTCTTCCTTCCTATC\n+TCCTTTTTATCAATCAAGAGCAGGAGGAGGGGTCTACACCCCCATGCCCA\n+CATGTGTGGCAGCAGCAGGCCCCATATTAATTTTGACTAATGTGCACTGC\n+TTTTGCCCTAAGTGCTGAATGGATGCAAATTTCTCAATGGAGGGATGACT\n+CAATTGGTTTTCCTGGAACATTCAGTCCTCTAACATAATGTGAATAGTCC\n+TACAAAAGGCGTTACCCGATTAGGCCTTCCTTCGGAGATAAATCCTAGGG\n+AGCTCAGAGCATGTCTGTCAATGGTGTGTACTAATCTACTTTGGAGGGAC\n+ACACATGATGCGGTGACTTATTGACTTCCCGATTGGTCGATCCACAGGAT\n+CCATTTGCTTTACCAAGCCATTATTTTCCAGGAGGTTGGCCTTTTGGCCT\n+GCTCCACTTCCATTCACCTATACACTTGCATTTAAGCTTGTATTATTCCA\n+CACCTGGAGTCAGATATGATTGTCTTAGGATGATTCAGTTTCACTTGCCT\n+ATACACCTGCATTTGCACACTTGAAATCTGTAGTCCAACTAGGAACACAC\n+TTTATACATTAGTAAAGATGACCACTTTTCAGGGCATTGCCGACCAGGAC\n+CAGAGACATCACAACAAGTGGTTCACTCTTTGTACTTTTGGTTATGGACA\n+CCTGCTATATTTCTACTCAATGTCAATACGATACATCCACTGATAAACAG\n+TCGATACACCATTGATGCATCCATTATGGAGGGGTCCACTTCTCATGCCC\n+ACATACACATGCTCTAGGATAGGGAGATACTTGTAAGCCACCTCAAGGTG\n+ACGCTAACTCTTTTCAATAAGTGTTTCCTGAACAATTTCACAGTGTGCTC\n+TATGCTGAAGAGACTTCCCGACATTCCATGCCCCCCCCCCATAATATGGA\n+CTGTGAAGAGCACTGGACCAGGTAGCCTGGATGGTCTGTTAAACTATAGT\n+GGAATGTATGCATTCTATATGCACTCCCAATTATGTGGCTTTGCTATCAG\n+CTATCAGAACAGCTAGCCAATCTCTCAAGCCTCCAAATATTGCTGACACA\n+TTTCATCCAAAGTAATGTAACCCCCACTTTAGCTAGCAAGAACCAACCTC\n+TAAAACTGGCCTATGTATATACTCACATCAAATTTACCAGTTGTAGGTTC\n+ACCTAGTAGTGAGTTGTACAAATTAGGTGGGGGGCTGAACTAATCACATT\n+GATCAACCAAGAAGAATTGCTATATACCTCCTAATCCTATAAAGTAGGAT\n+CTCTACAGTAAGAGTTCCAGACTCTGTCTGTGTCTTGACAGACGAGAGCT\n+CTTGGTAATCCATTCCATATAATGTGCTAACAACTCAGTCACAAAGGTCT\n+GCAGATTAGAGATGGGTATCTGATGACTTATTCGGACGCTTTAGCTTACA\n+GCTAACTCAGAACCCAACATCACTGGCATGATTTTCATTTTAATTGGAGA\n+AATGATGCCCATCATTTTCATATTCTTTGTGCCACTGAATTTTCACGCAT\n+GCCTAGCCGTATGTAGCATCTCCAATTTGGAAGTTCTTTCCTGGTTAACA\n+AAGGTTGGTAAATCCTTTCCTGTTAAGTCAAATAGTTGGTAATTTATTCA\n+TGTTCAAGAAGTTATAACTTAACTTATAACTTATTCTAGTCCCCCAGTTG\n+CTAGAGGGGTGCATTTAATCACCTGGGGAGAGTGTGTGCAATCTTTTTTT\n+TATTCCATGTCAGAAATGCATAAGGGAGTTATCTGTATTGGATTCCTCAG\n+CAGGGAGTTATCTGTACCTGATACCTGCCAACAGCATCAAAGGTTTATTC\n+TAACTGCGAACCCTCCTGAATAGTCTGGGCAGCCTAGTGGCCATCCCCAC\n+AGGTGAGGAGCCAAAGTTTAGAAGCTAAAAATTTATAACTACATCAAACA\n+CAAGAAGAAAAGCTATAAGCAGGCCAACGAAGGTGAGAAATACATTGTAC\n+CAGGCCAAGTGCCAACAATCTCCCTTATTGAATGCCTTGAGTTTCAAGAG\n+GGGTTCAGATTCATATGACCCCCTTTCTGACTGTTAGCATGATGTGATGA\n+CATGTGGCAACATGATACTTATGCAGATATTCTAGTATTGGGGCACCAAC\n+TTGCCAGCCAATCAACTGGTCCTGAAGATCATCAGCCTCATGTGGATAAT\n+GCCAAAGATGATAAGCATTGTTGTGGCCCATGTTATATGTAAAAATTAGC\n+TCCCAGCCCAGCAAAAGTTTTGTGCATTTGAGACCAGCTCACTGAAGACA\n+CCATTATGAGAAT\n'

diff -r 000000000000 -r 85f68b344286 test-data/simMouse_chr6.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/simMouse_chr6.fasta Mon Apr 04 06:27:44 2022 +0000

b'@@ -0,0 +1,12727 @@\n+>simMouse.chr6\n+TTTTTCAGTTGCAATACCCAACCGGGAGAAACTTTCAGTGAGCACACCTC\n+AGGTTCCTATATCAAGCAGGCAGTCTTGCATAGCAAATGGTCTCTGGTAG\n+ACGGTGCACTCAATCTATGTGAGGTATAGAAAATAAAGGACTACACACAT\n+CTCATCAAGTATCCCGTCATATTTGTGGCAAAACACACGTACAAATGCAC\n+ACTTGATGGTACTTGCCTGGAATATGACTCTAGGTTGATCCCTGGCACAC\n+AGGCACATTAATTCCCGAATGATGGTCTGCCTGTCCAGTTCTAGATAATG\n+TTACATTGGTGAACTTAAAACACAGAAATGACACATCCTTTTTAACCAAG\n+CCTAAAGTACAGAAAGTGAATGTCACCCTTGTTATATAAACCAGTATATA\n+GGGTAGCCACTGCTCTCTTAGCATTTATTTGCTGTAAAGGAACTGATGAG\n+CTAAAGTCGTCCAGAATGTATAAGCAGAAATTTGTAACCAGCCTTAAAGG\n+CAGCAGCTTTGGTTATAACGCACAATTCAAGACCACCTGCTGGATCCAGC\n+TACATTTAGCAATATTACTGATCTGTTGCACAGCAATCCATCAGGGTGAT\n+AGAAATGCAACACACATAACTTGTTGTCCAAGAGGTTAATTATTGTAAGC\n+GCATCTACATCCATCTATCAGTGGTCCTCTCTATTCAAGGCTCAAAAACT\n+CGTAGACTATTAGGGTCTCCAATAAACTATAAGGGCGATAGGGAACTCTA\n+GCTTTTACTTAGCACAACAGTCTATAGCCTACAACTGGTCACCAGTCACT\n+TTTCTTCTAGCAACAAGGTACAGAGGAGGGCTGTGTGGTGGTGAGTGATG\n+TACACCTTGGCATGAACCCACTGTAGGTAGCAATACTCCAACTGAAGTAT\n+TAGCCCGAGGAGAAATGCAAGTGCGAGTCCGTGCTATTGCAAAATTGGTA\n+TATATTCAATTTACTGGCCTTAGCTGCATTCCCCACAGTATTACATACCA\n+ATAACCCACATGGTCTCTAAAGACTCTGTTTCGCTTTGGATGTTGACTCT\n+CATCTATGGGCCAAACACACCTTTAAACTAATCTTCACCTTTCAAGTGAT\n+CTTGTGTCTCTATTTGCACAGAGTAAGATTATTGTGCGATTGATAGGAGC\n+ACTTGTTGGTAATTACTATCagactggattccatattgctcactcagtta\n+tcaggatgcaatatgactcaagtagtcccaggttttaaaccatcagAGCT\n+CACTGATAGGGGTTTGCTGGGAACCTATATTGATCCAGGGAAGAGGCCAC\n+CTGCAACATGTGCGCCTTGTCTACTACATGTAGGATTGAAGTTGTCAAGA\n+TCGAATCTTGCAGAGAATCGGATACTTTGTATAGTTATCTCATTCTCTCC\n+TCCACCACATTCTCTCCTCCACCACTACCTCTCAAATAGCACCTTCTGAA\n+TGCCAACTAGTACTCTTATTTTGCTTTTTCAGATCTACAATTAGATGTGT\n+TAGGTGCTCCCATATAGGGACTGCTCCACCATGAAAAAGACTGAACACCA\n+TGGTGTATAGCATCCTTTGACTGATGTTCTACAGTATTGTTTAAACATTA\n+CCTGTTCTAGTACACTCCATGGTACCTTGACTACATTCTGAGGGATTCCT\n+TCTGTAATGTTAACACTGTTCCTAATGACTTATAATATAGTTTACTAGAT\n+AGTATAATTTACTAGGTGAGGAGTCATGTTGCTCCCACAGACAAAATTAA\n+TTCAACAGGAAGTCTGTAACCCAATACAATGCTGGCAGTGAAGTATGATT\n+AGTGCTGTCAATTAATCATGATTAAATGGCCTCCTTGAACGGGCTAGACG\n+TTTTGGAGCTGTAGTATACCTTCTAGTTCTTTAATGTTTTAGCTTAATTA\n+AACATATGCTATTGTGATTCACACTTTTCTTTGGCCTATCTGCATTATAC\n+ATTGAGGTTGAGAGTACAATAACACTTCTGTTGTGTGAATTGTACTGATA\n+GTAATATATCACCCTAATGCATGCATGTGATTGAGCACTGTGAAATTGAG\n+AGTCTAGAAAGGGGTAGTTCCTCAGCTCATCATAACTCGATCTGATACAC\n+ATTTGATACTGAGTACGGTGAAATTGGCACTCTAGAAATGGGTAATTCTT\n+CAGTGCATCATCATCCTTTGTGAACCACCTATTTGGTCCCAACTGAGATG\n+TTCACAATTAGCATAAAGGCGTACACACTAGCTGGATTATAGATGTATAA\n+TATAAATTGCAGTGCTTCCATAGGACAGAGACAGAAGTTGGTGACCCTTT\n+TATTTGTTTGTTCTCATCCCCTGAGCAAGGAGGTCAGCTTAATTCATGGA\n+ACAGGCAGGCCCGTGAAATTTTTCTTGAAAAAGTGCACCGGTCATTAGTT\n+GCATAGGAGCCACACTATAGGACTGTTAATGAACGAAATGGGGGGTAGAG\n+TCTCACATACACGAGATCAGTGTGATCCTTCTTAGCCTAGCTAAACCTAA\n+TGGGGAGTAGGCCTATTACAGGCTGCTTGTTGAGTTGCATGCTGGAAACC\n+ATAGGTTAAGTGTGACTTGCTTTGGCAATTTGAGAAATACCACCCTCGGT\n+TAAGTGTTTGGTTATAAGTGTCATTTTGAGGGATGCCAGTTTTGACAAGT\n+TCAGGTTGATCAGGTTGATAGAGTGACCTTTCTTTGCATAGTGGACTTCC\n+AGACCTTATCAGCCTGAGTTGACCCTGCCCCATGTGGCCATGTACACATG\n+GCCAGTGCATGGCTACATTTGCTCCATGTGGCCATGTACACACGGTCAGT\n+GCTTGGCTATGAGCCTGCCCCACTTGATGAAATGTCAAATGATCTCCCCG\n+CATACATTCTGCATCCCTTGTCCGATTCAGGCACTGTGAAGCGATGACAG\n+ACCCCCGCGTACATTGTCGCCAGGATTAAAAGTTCACCTCATGATTTTAC\n+AACTCCATTCCCCTAACTGAGAGGATATTACTTATATAATAATACTTGTG\n+ACTGATACAGAGAATCACATCTATCTTGCCTTGTACCGACTAGAAACTTA\n+AATAGGATTACAGGATAATTAGTGGATTTCCCCTACTGGTACTAATCAAT\n+GTAATGAAGGTTATCTCCACAATACGAATTATAGCTTTTCAAGACAAAGT\n+ATTACACCTGGAGCATGAAATGTGCTTGACCTTGAAGAGATAAAACCCTA\n+TTAGCATACAGCTAGTGCTGGTCAGGTCAGCACATGTCTCAACAAACTAT\n+TAGTAGAATTATCACTATCAGTGGAAATTATATATCCTAGGGAGGTTCCT\n+CAATTCCAGACCGTTGGTTGAATCTTTGGCATAAAAGCATTGAGGATCTG\n+TTCTTCATCGTGAGTCCAATGGGACATATAGATCTAATCAGATCTGCAAT\n+ACCTAGCATGATAAAGGTTGACCATGGAACTTGGCCATAAAAAGAAACCA\n+TCCGATCTCCCAAATCCCTGAGTTCAGTAGATATTAGTGGGCACAGGCAT\n+TATGTATTCACTAGCAATAGATACAGCAGCTACGATAGTTGTGCTGTCTG\n+CATTGCCCATTTTACATTTGCATACCTGACCATCAATCCCCTACCAAATC\n+AACGATTGATATATGCTCCCAATGCTGTTCAATACAAAGGTCCAAAGTAC\n+ATTCCCTAGAGAATCTAAATAGAAGGTGTGCTGTGTATTTAGGTTTGCTT\n+GAGAAGCACGCTGCTATCACCTCACTCCTCTGTAAGTTCAATAGCCTGAG\n+GCTCATTTCCTCACAAAACATCACAAATCAAAACCACACTCCTCCGTAAG\n+GTCAATAGAC'..b'TATCAGATGTGCTAATGGTAACAACTAGATGA\n+GCTGAAGTAATTAGTTAGGCATATATAGTGGCTTTAATGAAAGTGTGGTG\n+AGGAGAAAATGAACTTGTTAATTGTTAGGTTGTATTAGTTAGTCTTGGCA\n+TTGGATTTGCTGGTCAAAGGTATATTGCCAAGACTATCTAACGAGGAATA\n+TAGGTCAGGATTGGGGGTTATTTATCGCCCTGTTATAGAATCTTACCAGG\n+GGACCCATGGTCAGGTTTTGCAAGTGCAAAACTTCATCTGGCCAAATGTG\n+CAAAAGATAAGGACAAATATTACTCCCATTTGAGGGTCGAAAATTTTAAC\n+AGGGTAGAACATTTTAACTCTTAAAGTTATCAGGTATACACCCTTGATTC\n+AGCTGTCCTTTTATACATGGCAGTCTCTTTGTGTTCTCGAGTGTGATGTA\n+CTGGTTGTTTTTGGGCAGACTAATGCACCACTTATAGAAAGCACTTGCCA\n+AGTATTATGGGAACTTTCAAGAGTTTAAATGCTTGTAGAGTGCTTTTAGG\n+GACCGCACTGTAAGCATTTTTGAGTTTAGAGCAACAGTGAAATTGGGAGG\n+TAGGACATTTCCTATGGAACCCGTCAACAGCATGGTCCTAACCCCAGAAT\n+CCATGTCTACTACTATATAGTCTCGCGATGAGAGTTAAGACACCCACATA\n+GGACATCTACTAAATACCTTAGTATAAACCTTTGACTACGCTACGTTGTC\n+CTTCCCCTTCATTGCTTCCCACCTTTTATTAGATGTCACAGCGCTAAATA\n+TTTCATATATCAAACCCATGCTTACCAGTTTATCTCTTGTTTTTGACCAG\n+CTATTAAGAGGTCACAATGCAATGTCTTTTAAATGGAACAGTAGCTAAGA\n+GGTTGTCTCTTATTTAATAAGCTGTAAAACACTGTGGACTACCTATCACT\n+AGTTAGTAGTCCCTCCATAGCAACTACTAGATATCATAAGGACAGGAGAA\n+TAGAATAAATAGATTCCTTGTAGACTAATTCTAATGAATCAAGACTGGGC\n+TGCCTGGAATAGTTTGCATATAATGCTGTCAAGCGGATTTTGTGTAGATC\n+ATCCAATGATCTGCGGCCACGAAGGGCAAACCTGTGGCGGTTAAAAAGGC\n+ACTAATTTCTCAATGGACAAAATTGTCTGATAGAAGGCTTAGTGATTCAT\n+GATTGTGTAGAGGCAGGGAATATGGGAATGCTCTGATTTCATGGGGGAGG\n+CTTGATTGGTTTTCCTTTGTGCAAGTGACCTGACTGGAAAAGCAAATGGT\n+GTACCACTGCCCACTAGGTCTTGCAATAATCTAGGGATGATTGTTTAGGG\n+TTAGAACATAGGTATTTGATTAGTCTAATGACTAATGCATAAAATCTGCT\n+GAATATTTAAATTTGTGCGGATAATTCAAAAGGTAAAGTGAATGGCCCAA\n+TGATTTGGTTCCCAGATGTTACAATCTGACAACCTAATATGACTAGTCCT\n+CAAAGAGGGACTATACCATTAGACCCTCCTTAAGAGATAATTTATAAGTA\n+GAAGTCTATCGATGGTGTGGGGTAATCACCTTTATTCACAGTGAAGTACA\n+ATGTGAGACTTTGGAGCGAGCGGCTGTCCTCGCCTTAACAGGGGACACAC\n+ATGGTGCGTTGATTTATGTACTATCTTGCCGGACAGTCGATACTATTTGT\n+CTACCTTTTAACGGTACTTAGACTTTGTACAGCGCCTCGTGCAAATCTCC\n+AAAAAAAGGCAAACACAGCCATGTACACACAATTAGTGCTTGGCTATGAC\n+CCTTCCCTGCACGACCATGTACAAACAGTCAGTGCTTGGCTACACTTGCC\n+CCACAAGTTTGCCCTGCATGATGAAGTGATCTTGGCGCGCACATTGTAGA\n+TCCCCTCTCTAGATTTGTGCACTGTCAAGTGATGATAGTCCTTCATGTAC\n+ATTGTCTTTGTGAAGCCATTTTTTTGGCTCAGCATTCTAGGCTGCTTCAA\n+GTTCCATTTACCAATACACTCACATTTACAATTCTATTTTACATCTCGAG\n+TTGGATAAGATTAGACCTCCTAACAGGTGCTGCCCTCCTTACATTTATAA\n+TTAGTAGCACCTGGTATATTACTTCCCAGCTATGCATGAACCGCTTGTGT\n+GAGGTGGGAAGACTCCTTCTGTGATCACTATTGCATCCATGCTGTGAAGC\n+TTTGCCTGTCAGTGGACCGCAATTCCTCTTGGTCAATCACTGTGGCCAGT\n+CCAACCCACCTGTTGGTCAGAAAGGAGACCACGCCAAGCTGGGATTCAAG\n+GCAATCAGGTGTTGGATCCCCCCACTTAATTGGCAAAGATCAGTGCTATG\n+CAGATCCACACTACACACCCAGGCCAGTTGCATCGGTTGGTTGTTTTTTC\n+TGATTGGGATGGGATGTGGTCCCATATGTAGCAAGCAATGTCACAGCAGG\n+CGATGAATGGCACATAGTTGGAGGTTCAAAACTCAGCTAGGCTGTTCTTT\n+TAGCATTGAGCACAAGATCGCTTAGAGGGGAGTGTACATAAAATGGGTCC\n+ATTCCTCAACAATTTAACAGACTACTCACCCACAATTTAACAGACTACTC\n+ACCCTACTTTGGTCACGGCTCTATTTAGTTGATATGAGGGAGGAGCAGGG\n+AATCTCGATGTAAAATGATCGAGAAAGTGTCAGTTATCTCAAAAGATTAA\n+ACTAAAGCACAGGTTTGAGTAAGCACAGATTTGAGTACAACTTTGTATTT\n+GTAGACAATAGGTTAGCCTGCTCTGGGAGAGAGTTACTAGTTTCTCCCCA\n+TAGAAGATAAGTTCCACATATTTACTTGTATATATGTAGTTTAATGATCC\n+CCATGTCAGAAAAGCAAGAAGTGGCTTCTTAGAAACTTGTTTCTTGATTG\n+GAGACTTGTGTGTGTCATCTCTCTGTCATGTACATGGCTGCTTGCCTTTT\n+ATTGGAGCTTTGCACGAGACACTATGTGAAATCTAAACAACATAAAGCTA\n+AAATCTAAAATTCTTTGCAAATAGTGGGCACGAAAGTCGTTATAACCAGT\n+GAGTGCTACATCGTACTGTCTGGGCCCACGGTCATGATTCGCTCAAGACG\n+ATTTGCTAACTGAGCGCTCTGGTATGCGACCGCCTTGCGTACGCTTTGTT\n+CACGACTTCGAAGTCTCTGGATTTACTATGTGTCCATGGAGTTATGACAG\n+GTTTGAGTCTCCAAACACCAGGAATCTGTTTGATCCTGAGGGTTTGTAAA\n+AGGGACTCTTGTCTCTACTAGTTGCCTCATCAGCCAGCAGATTATCTGTG\n+CTTGATACCTGCCATTAGTGTGAAATGGCTATTCTTACTGTAACCCAATT\n+GAGTAGTTATGTGATGTAGTGGCCATCCTGATAACAGACGAGATGCCATG\n+GATTAAAAGTGAAAAATTTAAAACTTATCTGAACACAAGATGAGAACCTA\n+TAAGTTGGCCAAAGACAGTGAGAAATACCCTGAACCAACCTAGGTGTCAA\n+CAATTTCTACAGTTCGGTGCCTAAGATCCAAGAGAGGCCCAGTCCGTTTT\n+GACCCCTTTGCTAGCTGTAACTACGATATTGTGATGTTTGGCAGTATCAC\n+CCTCACACTGAGACTTTAGATCTGGAGCAAGTACTTTTGTGCCATAGGCC\n+CCTGGATGAACCACTCAAGAACATTATGAGCGTTATAGGGACAACATATT\n+ATTAACCTCATGGAGACATTGTGGCGACATTGCCAAAGATAGAGATATTG\n+CCAAAGATATATTGAATACTGTTATCCCATGTTATATTCACAAACAACTC\n+TCATCCCAACGAATGCTTTGCACACATTAAGACTCACAAATTGAAGACAC\n+TGTTGTGAGAAT\n'

diff -r 000000000000 -r 85f68b344286 test-data/simRat_chr6.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/simRat_chr6.fasta Mon Apr 04 06:27:44 2022 +0000

b'@@ -0,0 +1,12946 @@\n+>simRat.chr6\n+TTTTCGGCTGCAATACCCAACCTGAAGACATTTTCAGTGGGCCCACCTCA\n+GGTTCTTATATCAAGCAGACAGTCTTGCGCAACAGATGGTCTCTGATAGA\n+CAGTGCACTCAATCTATGTGAAGGATAGAAAACAAAGGACTACTCATCTC\n+ATCAAGTATCCTGTCGTATTTGTGCTTTAGACTCAGCAAAACAAGTGTGC\n+AAGTGCACACCTGATTGTACTTGTCTGGAATATGACTCTAGGTTGAGCCC\n+TGGCACACACTCAGGTCAACTCCAATGATGGTCTGCTTGTCCAATTCTAG\n+ATAAACATTACATTGGTGAACTCACTAAAACACAGTTAAAATTACTAATC\n+CTTTTTAGCACAGCCTAAAGTACAGAGAGTGAATGTTACCCTTTTGATAT\n+GCATCAGTATATAGGGAGCCACTGGCCTCTTAGCATTCATTTGCTGTAAG\n+GTAATGATGCGCTAAAGTCATCTAGAATGTATAGGTAAAAGTCTGTAAGC\n+ATTGTAAAGGCACCGGCTTTGGTTATGATGCACAATTCAAGACCATCTGC\n+CCAGTTAATTAGTGTGACTGGATCCACATCCACCTATCAGTGGTCCTCTC\n+TATTCAAAGCTCAAAAACTAGTAGAGTAATAGGGGATCCAATAAACTTTA\n+AGGGCGATAGGGAACTCTAGTTTTTACTTAGCAAAACAGCCTACAGTTGA\n+TCTCCTGGATCTGGTCATCTGTCACCTTTCTTCCAGCAACAAGATACAGA\n+GTAGAGCTGTGGGGTGGTTAGTCATGCGTACCTTAGCATGAGCCCACTGT\n+AGGTAGCAATCCTCCAATTGAAGGTTAACCCAAGGAGAAATGCAAATGGG\n+AGTCCATGCTATTGTATATTGTTATATATTCAATTTGCTGGCCTTAACTG\n+TATCCCCTGCAGTGTTACATACCAACAACCCACATGGTCTCTAAAGACTT\n+TGTTTTGTTTTGGATATTGGCTTTACCCTATGTGGTGAAGCAAACCCTTA\n+AACTGATGTTCACCTTTCAAATAGTCTGGTGTCTCCATTTATACAGAGTA\n+TGGTTATTGTGGGATTGTCAGGAGCACTTGTTGGTAATTGCAACCAGATC\n+GGATTCCATATTGCTCATTCAATGATCAGGATGCAATATGACACAAGTAG\n+TCCCAGGTTTTAAGCCATTAGAGCTCACTGATGGAGGTTTGCTGGTAACC\n+TAATAGACCCTAGGAAGAAGCCACCCACAACATGTGCACCTTGTCTACCT\n+TATGAAAGATTAAAGTTGTCAAGATGCAATCTTGCAGATAATTAGATACT\n+TTGTACAGTTATCTCATTCTCTCCTCCAACACTACCTCTCAAATAGCACC\n+TTCTCAATCCAACTAGTATTCATATTTTCCTTTTTCCGGTCTACAATTAC\n+ACCTCTTAGATGCTCCCATATAGGGACTGCTCCCCCATGAAAGAGACCAA\n+AAACCATGTGTATAGCATCCTTTGACTGATGTTGTACAGTATTGTTTAAA\n+CTTTAGCTGTTCTAGTTCGCTCCATGAAACCTTGACTACATTCTGAGATA\n+TTACTTCTGAGCTGTTAACACTGTTCCTAATAGCCTATAATATTGTTTAC\n+TAGATATATAGTTTACTAGGTTAGGAGTCATGTTGCTTTCACAGACAAAC\n+TTAATTCAACAGGAAGTCTGTAACCCAATACTATGAAGGGAGTCAATTAT\n+AATTAGTGCTGTCAATTACTCAGGATTAAATTGCCTTTGAAAGGGCTAGA\n+TCTTTTGGAGCTGTAGTCTACCTCCTAGTACTTTAATATGTTAACTTAAA\n+CATTTGCTATTGCTATTTACTTACCTTAAACATATGCTACTGTCAGTCAC\n+ACTTTTCTTTGGGCTAGCTGCATTATATGTTGAGGTTAAGAGTAGAATAA\n+AACTTCTGTTGTGTGAACTGAACTGACAGAAATGTATCACCCCAATGCAA\n+GCTTGTGATTGAGCAAGGTGAGATTAGACTCCAGAAGAGGTCATATGGCA\n+GCCCATCATAGCTCAACCGGATACACCCTCAGGAATGATTAGGGTGAAAT\n+TGTAGAAAGGGGTAACTCTTCAGCTCATCATCATCCTTCATGAACCACGT\n+CTTTGGTCCCAACCGAGATGTTCACAATTTGCCTAAAGGCTATAGGTTAC\n+ACTGACTGGCTTAAGGATGTGCAATATAAATTGCTGTGCTTCCATAGGAC\n+AGAGAACAAAAGTTGGTGACTCTTTTTTTTGTTCATTCTTGTTCCCTGAG\n+CTGTAAAGCAAGGAGGTCGATTCATGGGACAGGCAGGCCTGTGAAATTTT\n+TCTTGATAAAGTGCCTTTGTCATCAATTGTGTAGAAGCCACACTAAAAGA\n+GTGTTAATGGACTAAATGGGGGGTAGAGTCTCACATACATAAGATCAGTG\n+TGAACCTTCTTAGCCCAGCTAATCCTAATGGGGAGTTGCCATTACAGTTT\n+GCTTGTTGAGCTGTGTGCTGGAAACCTTAGGTTAAGTGAAACTTGCTTTA\n+GCTATTTGGGAAATACCACCCTTGGTTAAGTCTCATTTTGCAAAGTTCAG\n+GTTGATAGAATGACCTTTCTTTATGCATAGTAGACTAATTGGTGTACTCA\n+AATGACCTCCAGACCTTATCGACCCAAATCCATTGTGTTATAACACTATT\n+TAGACTTCGCACAGCGCAGATGCGGCCATGTACACATGGTCAGTGCTTGC\n+CTATGACCCTGCCCTGCATGGCCATGTACACATGGTCAGTGCTTGGCTAT\n+GCCTGCCCTGCGTGGCCATGCACACACAGTCAGTGCTTGGCTATGAGCCT\n+GCCCTGCATGACAAAATGTTGGGTGATCTCCCCGTGAACATTGTAGATTC\n+CCCTGTCCTTTTCACGCACTGTCAAACAATGACAGTCCCCTGCGTACATT\n+GTTGCCATGATTAAAAGTTCACCTCATGATTGTACAACTCCGTTCCCCTA\n+ACTGAGGAGATGCCACTTAATAATAATACTGGTGACTGATACAGAGAATT\n+GCATTATCTCTCCTTGTACAGATTAGAAACTTAAATAGGACTACAGGACA\n+GGATATTTAGCCGATTTCCACACTGTAACTATCCAATGTGATGAAGGTTA\n+TGTCCACGATACTAATTATAGCTTTTTAAGACTAAGATCTATTACACCTG\n+TGAGCAGGCAATGTGCTTGCCCTTGGAGAGATAAAACCCTAATAGGATAC\n+AACTAGTACTGTTGAAGTTAACACATGTGACAACACACGATTAGTAGAAA\n+TTATCACTATTAGTAGAAATTATGTATTCCTGGGAAGGCTCCTCAATTCC\n+AACCCTTTGGCATAAAAGCATTGAGGATCTGTTCTTCATGGTGAGCCCAG\n+TGGTTAGTTGACATATAGATCTAACCAGATCTGTGGCAATATCTGCAATA\n+CCTAGCATGATAAAAGTCAACCATGGAACTTGGCATTATAAGAGGAAATC\n+ATCCGATCTCCCTGAGATCTGTAGATAGACATTATGTCTTCATTAGCAAT\n+AGATACAGCAGCTACTATAGTTGTGCTGTCTGCATTGCCCATTTTACATT\n+TGCCTCCCTGACCACCAATCCCCTACCAAGTCTATGATTGATAAGTGTGA\n+ACACTGTTCGATGCAAAGGTCACCCAAAATACATGCTCTAGAGAATCCAA\n+ATAGAACGTGTGCTGTGTGGATAGGTTTGCTGATGGTAAGCATGCTGCCA\n+TAACCTCATGCCTCTATAAGGTCAATAGACTGAGGATTATTTCCTAACAA\n+AACATCGCAGCTCAAGGTCTCAATTCTATCACTGGTGGAACACCTTGTGT\n+GAAAAGTTTGTG'..b'ATGGTAACTGAAGACCCAGCCTTGGGAAA\n+CCGAAGTATCACCCTGTCAGAGCAGCCCAATGGGTAGTCTCCAAGAGAGC\n+CTTCTAATCCCAAAATATCTGTCACATTGCCCATCCTTGTTCTTGTAACA\n+TAACTTATGCTTTTGTATATTCTACCCATCCATAAACTTTAGTGTTGCTT\n+TTGCATTTAAAGACAAGTCATGCTTCGTTTTCATCCTCATTTTGGACCCT\n+ACACGAATCCTGTAAGTCTAAATGAACTCATAGGCAACCTTAAGCTGCCA\n+CTTAGCTTTATGACATATTACATTTAGGTCACAAGTCCTGAGAGGTGTGG\n+TGGTGCTGAGATTGTCCAACTGTGGTCAACTTGTGGTCAACAACCATAAA\n+TCATATAGTATAAAGACTTGTTTAGTGTATCAAATGTGCTAATGGTAACA\n+ACTAAATGAGCTGAAGTAATTGGTTAGGTGTATATAGTGGCTTTAATGAG\n+AGCTTGGTGAAGAGAAAATGAACTTGTCCGTTGTTAGGTAGTATTAGTTT\n+GTCTTGGCATTGGATATGCTGGTCAAAGGTATTGCCTAGGCTATCTAACA\n+AATAATATGGGTCAGATTGGGGGTTATTTACCACCCTGCTATTGGAGTAA\n+TGCTACCAGTGTGACCGGGACCCATGTCATGTTTTGTAATTACAAAACTT\n+CATTTGGCCAAATGTGCAGAACATAAGGACAAATATTCCTCCGGTTAGAG\n+CGTAGAAAATTTTGACGGGGTAGAAGACTTCAACTCTGAAATTTATCAAG\n+AAGGCACCCTTGATTCAGCTGTTCATTTACAGACTAACGCTCTTCTTATA\n+GAAAGCACTTGGTAAGCATTACGGGAGCTGTCGAGAATTTAAATGCTTGT\n+AAAGTGCTTTTATTAAGACACCCTTCTGGGACATCTATCTAAATACCTTA\n+GTATAAAACATTGACTATGTTGTCCTTGCTCCTCATCAGTCTACACCTTT\n+TATCAGATGTCGCAGTGCTATATGTTCCATATATCGAGGACCCATGCTTA\n+CCAGTCTATCTCTTGTTTTTGACCAGCTATTAAGAGGATAAAGTGCAATG\n+TCTTCTCAATAGAACAATATGAGGTTTTCTATTATTTAATAAGCTACAAA\n+ACACTGTGGACTATCTATCACCAGTTACCATTGTGTTTGTAATCCCTTCA\n+TACCAACTCTAGATGTCCTGAGGACAGGAGAATTGACTAAATAGATGCCT\n+TGCAAACTAAGTGTGACGGATGCTGCTTGGAGTCGTTAGCATAAACTGCT\n+GTCAAGCGCATTTCGTGTAGATCATCCACTGAGCTGTGGCCCCCAAGGGC\n+AAACCTGTGGTGATTAAAAAGGCACTAATTTCTCAATTGAAAAAATTGTC\n+TGATAGAAGACTTCGTTGATTCATGCTTGTGTAAAGGCAGGCATATGGGG\n+ATGTTCTGGTTTCAGGGGGGAGGCTTGATTGGCTTTCATTTGTGCAAGTG\n+ACTCGACTGGAAAAGCAAGTGGTGTACCACTGCTCTCTAGGTCTTGCAGT\n+AGTCTAATGATGAATGTGTAGTGTTGGACCATAGGTATTAGATTAGTCTA\n+ATGATCAGTCTAATGACGAACATCTAATATCTGCTGGATATATTTAAAAT\n+TATGCAATTAATTTAAAGGGTAAGTGAATGGCCCAGTGAATTGGTTCCCA\n+GATGTTTCAATCCAACAACATAACATGACTAGTCCTACAAGGGGCACTAC\n+ATCATTAGAGCCTCCTTCAGAGATAAATTATAAATAGTAGAAGTCGATCG\n+ATTGTGTCAGGTAACCATCTTTAAGGGGACACACACGGTGCGTTGACTTA\n+TGTACCTTCTTGCCGTACGATCCATACCATTTGTCTACCCCTCTGTGGAG\n+CCAGTTTTCTGGATGGGGTCAGCCTTCTAGGCTGCATCAGTTCCAGTTAC\n+CAATACACTCACATTTATGATCATACTACTTTACATCTTGAGTTGTATAA\n+GATCAGACCTCATAACAGGTGCTTCTTGCCATACATTTGTAATTACTCGC\n+ATGATATATCTCTTACCAGCTATGACGACAAACCACTTGTGTGATGCGGG\n+CAGACTCCTTCTGTGATCATTTGACATCTCCTCAAAAGGGGCTGGCTCAT\n+AGCCGAGCACTAACTGACATCAATATCATACAGCCACACCAACCATGGTT\n+TCAACCATTAAATAGGACGCATGCAACCCATCTGTGATAGGGAGAAATTA\n+GTAAGTCTCTTCCAAAACAGGCTTACCTATTGCTTATAAATACAAAGTTG\n+TACTCAGATCTGTGCTAATTCAAACCAATGCTTTGGGTTGCTCTTTCCAG\n+ATAACTGACACTTCGTAGATCATTTTATAGTGAGATTCCCTGCTCCTCGC\n+TCATATCAACTGAAAAGAGCCCTGGCCCGAGTAGGGTGAATAGTCTGTGT\n+TAAATTGTTGGGGAATGGAAACATTTTATGTATGCTCCCCTCTAAGTGAT\n+CTTGCTTGAGTAGCTAACAGTACAGCTTAGCCAACTATCAACCATTTATT\n+GCCTCCTATGACATTGCTTGCTACATAACAGGACTGCATCCCAGTCAAAA\n+AATACAACCCACCCATGCAATACAACCCACCTATGCAACTGGCCTGGGTG\n+TGTTATTGTGGAACTGCATAGCACTGATTTCTGCCAATTTGGTGGGGAGA\n+TCCCACCAGATTGCCCTTAAATGTGACCAACAGGTGGGTTCATCGTCCAG\n+GGGCCTATGGCACAAAAGTACTTGCTCCAGTTCTAAAGTCTCAGTGTGAG\n+GGTCATACTGCCAAATGTCATAGTATTGTATTTACTGCTAGCAAAGGGGT\n+CAAGAGAGTCTCTGTGCCACTTGTGAACCTCAGGCACTAAACTGTAGAGA\n+TTGTTGGCGCCTAGGTTGGTGCAGGGCATTTCTCACTGTCTTTGGCCAAC\n+TTATAGGTTCTCGTCTTGTATTCAAATTAGTTCTAAATTTTTTGCTTCTA\n+ACCCTTGGCATCTTGTCTGTTATCAGGATGGCTAATAGAGCACATCAATA\n+CTACTCAAGTGGGTCGCAGTAAGAATAGACCATTTCACACTACTGGCAGA\n+TATGAAGCATACGTAACCTCCTGGATGAGGCATCTAGTACAGATATCCCT\n+TTTGGATGGTGGCTTGGAATAGAAAATTACAAAACCTCAGGATCGAACAG\n+GTTTCTGGCGCCTGGAGACTCAAACCCAGTAAAACTCCATGGCCATGTAG\n+TAAATCCAGAACTTGGTTTCGCATCTGTCTCCTGACACTCGGATTTTTGG\n+AAACTGATGCCACGGGGGGAGACCGATTTGCAAGGAATCTTAGCTTAATG\n+TTGTTTAGATTTCACATAGTGCATTGTGCAAAGCTCCAATAAAAGGCAAG\n+GGGCCATGTACATGACAGAGAGATGACACACACAAGTCTCCAATCAAGAG\n+GGAAGTTTCAGAGAAGCCACTTTTTATTCTTCTTACATGGACCTGATTAA\n+ACTACATTCATACAAGTAAAATTTCGACTTATCTTCTCTATGGTTGGGTC\n+ATTACCATGAAACCCCACCGATCATATGGAATGGATTAGCCTCTCAACTA\n+CCCAGACGAAGATAATCTATCGGCTCCATGCTGTGAAGATCTACTTAGCC\n+TGTAAAGTGGACTGCAATTGTTCTTGGTCAATCACTGTGGGCAGTACCAC\n+TCAAGAACATTATGAGCCTTATAAGGACAACACATTGTTAGCCTCATGGA\n+GACATTGCCAAAGATGTATTAAATACTGTTATCCCATGTTATATTCACAA\n+ACAACCTCATCCCAACAAATGCTTTGTACACATTAAGACTTACATAAAGA\n+CATTGTTGTGAGAAT\n'

diff -r 000000000000 -r 85f68b344286 test-data/test_tree.nhx
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_tree.nhx Mon Apr 04 06:27:44 2022 +0000

@@ -0,0 +1,1 @@
+((simHuman_chr6:0.144018,(simMouse_chr6:0.084509,simRat_chr6:0.091589)mr:0.271974):0.020593,(simCow_chr6:0.18908,simDog_chr6:0.16303):0.032898);
\ No newline at end of file

diff -r 000000000000 -r 85f68b344286 test-data/vulg_25.fasta.gz

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

diff -r 000000000000 -r 85f68b344286 test-data/within.hal

Binary file test-data/within.hal has changed