# HG changeset patch
# User iuc
# Date 1711489777 0
# Node ID 1f08834f987e9cabe8e0d0cc78cbc04cbb598720

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit d3d2bb547caccd2d217e5b77d62ea181f8e870c7

diff -r 000000000000 -r 1f08834f987e macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Mar 26 21:49:37 2024 +0000
@@ -0,0 +1,21 @@
+<macros>
+    <token name="@TOOL_VERSION@">2.3.1</token>
+    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@PROFILE@">20.09</token>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">seqkit</xref>
+        </xrefs>
+    </xml>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">seqkit</requirement>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1371/journal.pone.0163962</citation>
+        </citations>
+    </xml>
+</macros>
+
diff -r 000000000000 -r 1f08834f987e seqkit_sort.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seqkit_sort.xml	Tue Mar 26 21:49:37 2024 +0000
@@ -0,0 +1,81 @@
+<tool id="seqkit_sort" name="SeqKit sort" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>FASTA or FASTQ files</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        #set $input_fn='input.' + str($input.ext)
+        #set $output_fn='seqkitsort_output.' + str($output.ext)
+
+        ln -s '$input' '$input_fn'
+        &&
+        seqkit sort
+        '$input_fn'
+        $reverse
+        $sort_by
+        -o '$output_fn'
+        --threads \${GALAXY_SLOTS:-4}
+
+]]></command>
+    <inputs>
+        <param name="input" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Input file"/>
+        <param name="sort_by" type="select" label="Sort by:">
+            <option value="" selected="true">Sequence ID</option>
+            <option value="--by-bases">Non-gap bases</option>
+            <option value="--by-length">Sequence length</option>
+            <option value="--by-name">Full name (instead of just ID)</option>
+            <option value="--by-seq">Sequence</option>
+        </param>
+        <param argument="--reverse" type="boolean" truevalue="--reverse" falsevalue="" checked="false" label="Reverse the result?"/>
+    </inputs>
+    <outputs>
+        <data name="output" format_source="input" from_work_dir="seqkitsort_output.*" label="${input.name} sorted (${tool.name})"/>
+    </outputs>
+    <tests>
+        <!-- 1. fastq.gz -->
+        <test expect_num_outputs="1">
+            <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/>
+            <output name="output" file="sort_output1.fastq.gz" ftype="fastqsanger.gz"/>
+        </test>
+        <!-- 2. fasta.gz -->
+        <test expect_num_outputs="1">
+            <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
+            <output name="output" file="sort_output2.fasta.gz" ftype="fasta.gz"/>
+        </test>
+        <!-- 3. by-bases, forward, fasta -->
+        <test expect_num_outputs="1">
+            <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
+            <param name="sort_by" value="--by-bases"/>
+            <output name="output" file="sort_output3.fasta.gz" ftype="fasta.gz"/>
+        </test>
+        <!-- 4. by-length, rev, fasta -->
+        <test expect_num_outputs="1">
+            <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
+            <param name="reverse" value="true"/>
+            <param name="sort_by" value="--by-length"/>
+            <output name="output" file="sort_output4.fasta.gz" ftype="fasta.gz"/>
+        </test>
+        <!-- 5. by-name, forward, fastq -->
+        <test expect_num_outputs="1">
+            <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/>
+            <param name="sort_by" value="--by-name"/>
+            <output name="output" file="sort_output5.fastq.gz" ftype="fastqsanger.gz"/>
+        </test>
+        <!-- 6. by-seq, rev, fastq -->
+        <test expect_num_outputs="1">
+            <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/>
+            <param name="reverse" value="true"/>
+            <param name="sort_by" value="--by-seq"/>
+            <output name="output" file="sort_output6.fastq.gz" ftype="fastqsanger.gz"/>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Sort sequences (FASTA, FASTQ) by id, name, sequence, or length.
+
+    </help>
+    <expand macro="citations"/>
+</tool>
diff -r 000000000000 -r 1f08834f987e test-data/fx2tab_output1.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fx2tab_output1.tabular	Tue Mar 26 21:49:37 2024 +0000
@@ -0,0 +1,5 @@
+1/2	TATACTACTGTCATGTTTGCTTTTTTCGTGCTCATTACCTTATCGTATGCTTCCATCCAAAGATCTAGTTGTTTATAATATTCTCCCGGCCTTACTTCAAC	?@<DDDADDFAAC@>GG<FDCBHIIGB:8??DEAHGAFEDF<B?F9DBFFCDHF>48BBCF)8877=@=@C7=E??EBD:AADA;>C3;BB6:A@>>@:3>
+2/2	AAAAAAACTTTCTTTACAGGCGTAAAGAAAGTGAAATTGACAGTATTTATACATGAAATAGCAATGTCTTTCCCACTTCCCTACGCTGGCATTAACCAGAT	<@@DA6DDF42ABGF9F?F@C<EDDDFBGI>04BGC>BFF><?*88BDFDEAFFDGCGEFEEFIFFFEF>EBDBB@@:ACCCAB8@?=;B<@BABBBBB?#
+3/2	GTGCCATCATTTTCTATCCATTATTATGGATTATTGGCTCATCGTTTAATCCGGGTGATAGTTTATCTGGATCAAGTATTATTCCACAAAATGCAACGTTA	=BBFFFFFHHHHHJJJJJJJJJJJJIJIJEIIGIJJJHGIGGIIGHIDIJGHIIJ?FFHGIIJJJJJJJJHGIHHHCEHFFFFFFFFEAECCDADDDDDDD
+4/2	TTCAAAACACATAAAGCTAATTGCCGCATATGACAATATTGCTAAAATAATTTTTTTACCAGATATCGGTGTTAATCGAAATAATGTACTTTCGGTCATTT	BBCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJIJJJJJJIJJJJJJIIJJJJJJJIJJHHHHHFFDDCDEEEDDDDDDDDEDDDFFFEDDDDDDDDE
+5/2	ACTTGCCAATGCGATGCACCAATCTTTTCAGCAATAATCGGCAAAATTGGGTCGACTACTCCTATACCTGAAAAGGCAAGGAAAGTAGCCAACACTGTAAT	BCCFFFFFHHHHHIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIHIIJIJHHHHFFFFFFEEEEEEDDDDDDDDDDDDDCDDDDDDDDDDDDDED
diff -r 000000000000 -r 1f08834f987e test-data/fx2tab_output2.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fx2tab_output2.tabular	Tue Mar 26 21:49:37 2024 +0000
@@ -0,0 +1,6 @@
+#id	length	avg.qual
+1/2	101	24.98
+2/2	101	20.44
+3/2	101	37.13
+4/2	101	37.61
+5/2	101	37.28
diff -r 000000000000 -r 1f08834f987e test-data/fx2tab_output3.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fx2tab_output3.tabular	Tue Mar 26 21:49:37 2024 +0000
@@ -0,0 +1,3 @@
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	GAGAGGACGAGGTGCCGCTGCCTGGAGAATCCTCCGCTGCCGTCGGCTCCCGGAGCCCAGCCCTTTCCTAACCCAACCCAACCTAGCCCAGTCCCAGCCGCCAGCGCCTGTCCCTGTCACGGACCCCAGCGTTACCATGCATCCTGCCGTCTTCCTATCCTTACCCGACCTCAGATGCTCCCTTCTGCTCCTGGTAACTTGGGTTTTTACTCCTGTAACAACTGAAATAACAAGTCTTGATACAGAGAATATAGATGAAATTTTAAACAATGCTGATGTTGCTTTAGTAAATTTTTATGCTGACTGGTGTCGTTTCAGTCAGATGTTGCATCCAATTTTTGAGGAAGCTTCCGATGTCATTAAGGAAGAATTTCCAAATGAAAATCAAGTAGTGTTTGCCAGAGTTGATTGTGATCAGCACTCTGACATAGCCCAGAGATACAGGATAAGCAAATACCCAACCCTCAAATTGTTTCGTAATGGGATGATGATGAAGAGAGAATACAGGGGTCAGCGATCAGTGAAAGCATTGGCAGATTACATCAGGCAACAAAAAAGTGACCCCATTCAAGAAATTCGGGACTTAGCAGAAATCACCACTCTTGATCGCAGCAAAAGAAATATCATTGGATATTTTGAGCAAAAGGACTCGGACAACTATAGAGTTTTTGAACGAGTAGCGAATATTTTGCATGATGACTGTGCCTTTCTTTCTGCATTTGGGGATGTTTCAAAACCGGAAAGATATAGTGGCGACAACATAATCTACAAACCACCAGGGCATTCTGCTCCGGATATGGTGTACTTGGGAGCTATGACAAATTTTGATGTGACTTACAATTGGATTCAAGATAAATGTGTTCCTCTTGTCCGAGAAATAACATTTGAAAATGGAGAGGAATTGACAGAAGAAGGACTGCCTTTTCTCATACTCTTTCACATGAAAGAAGATACAGAAAGTTTAGAAATATTCCAGAATGAAGTAGCTCGGCAATTAATAAGTGAAAAAGGTACAATAAACTTTTTACATGCCGATTGTGACAAATTTAGACATCCTCTTCTGCACATACAGAAAACTCCAGCAGATTGTCCTGTAATCGCTATTGACAGCTTTAGGCATATGTATGTGTTTGGAGACTTCAAAGATGTATTAATTCCTGGAAAACTCAAGCAATTCGTATTTGACTTACATTCTGGAAAACTGCACAGAGAATTCCATCATGGACCTGACCCAACTGATACAGCCCCAGGAGAGCAAGCCCAAGATGTAGCAAGCAGTCCACCTGAGAGCTCCTTCCAGAAACTAGCACCCAGTGAATATAGGTATACTCTATTGAGGGATCGAGATGAGCTTTAAAAACTTGAAAAACAGTTTGTAAGCCTTTCAACAGCAGCATCAACCTACGTGGTGGAAATAGTAAACCTATATTTTCATAATTCTATGTGTATTTTTATTTTGAATAAACAGAAAGAAATTTTGGGTTTTTAATTTTTTTCTCCCCGACTCAAAATGCATTGTCATTTAATATAGTAGCCTCTTAAAAAAAAAAAAACCTGCTAGGATTTAAAAATAAAAATCAGAGGCCTATCTCCACTTTAAATCTGTCCTGTAAAAGTTTTATAAATCAAATGAAAGGTGACATTGCCAGAAACTTACCATTAACTTGCACTACTAGGGTAGGGAGGACTTAGGATGTTTCCTGTGTCGTATGTGCTTTTCTTTCTTTCATATGATCAATTCTGTTGGTATTTTCAGTATCTCATTTCTCAAAGCTAAAGAGATATACATTCTGGATACTTGGGAGGGGAATAAATTAAAGTTTTCACACTGTGTACTGTGTTTTACTGATTGGTTGGATATTGCTTATGAAAATTCCATAGTGGTATTTTTTTGGATTCTTAATGTGTAACTTAAACATACTTTGAAGTGGAGGAGAGTCATAAGACAGAACATTTGGCAGGAATTGTCCTTATGAAACAAGAAAAAGAAAATGAAAAGTATTATTAAGCTTCTGTGTTTGTCTAAAAATGTGGCATATGGATGGCATTTAAAACTTTGAATGAATTATACCTAAATCTGGGACAGGGAGGTGACAGTGGAACAGGCTACCAATCAGAACTAGATGACTTTTAAGGCTCCTCCTATTATGAGACTTCAATTTCCAAAGAGAAGAACTAGCAGAGAAATTGTATTTCAGTAATTTTAAGCTCCTTCTGTCTTGTAGAGTCTTGTTATAGTTGTATAAATCAAAAACACAGAATAAGGAACATATTTAACTTTTTTTCATTATAAAATGGTTAGAGGACCCTACCCCCTCTAGATTCCCTGATTTCCCCAGGCCTGCAGCATACAGTAAGATGGGTCCCTGTGCCAGGCCTCAATACTGCCAGGGAATAAAACCAGAGGGAGAGGACCCTCAGTGTCATATCAGGAAGCCCAGTGCCAGAGGACAGACAGGTTCAAAACTGGCTTTTCCTCTGGGCCTGGGTTGGTGCTATAGGCCAAGGGTCATTTTATACTTGGGTATAAATCAATCCCAGTTTGGGAAAAGATTATTTTTAAGCTTAAAAGGCTGACATGTGCCATTATATGTAGTATGTAATATATGTAACATCTTCCAATTCTTTTAAAATAAAATTAATATTTATAATGGATATTTAATGATTGTTATTTTTAAAAACCAGCTTATAATTCCTCGTTATGCATGATTTATCCAAAGTTTCCATAGTTTTATTCAAAATAATAAATGTTAATAAGGTGATAAGGGGTATATTTAATGTATTGTATCAAATTGTGAATAAGAAAGTAGGATGGAGCTTTCTAGAGGTTGGGCCTTAGTTCTGTTATCCTCATTGCTTTTAACCAATAAGTTAAATGAAGTTAGAGTTATGGTCTTCAGGTTAGATTATGGACCAGATCTGTGAGGGTCAGCATGGAAATTCACATTCAACAAGGTAGCACACAGGACCAAGAGCAGCACATGCAATCAACTGGAATAATATAGTAATCCTGTAACTGGGTTTGAAAAAATAATCAACAAAAGATACAATTCAAGGGTTAGGTTGCAGAGAGCTGGCTTGAGAGTAGTTATTATGAAAAAGGCCTCAAGGAGTACGTGTTCAGTATGCTCTAAGATGATAAAGTGGCTGTTAAAAAGGGAGTTGATTTGAGGAAGTATTACTTAGCATTCATGCATATTGGGCTTAGGCTCTAGCCCTGCCACTATCATTGTCTTCTCTGGACTGTGAAGTCACTGAGGACAAGGAAACTAAATTTAATGTCTGTATCACTAGTGCCTAGAATTTCTGGACACTTAGTAGTCACCATCAGGCGTTTATTTAATGAATGAGAAGCAAAGTGACCTTGGTTACTTTTTTACCCTGAGGGGCTCAGCACTCATTAGGACTTGGTGCCTAATTTTATAAAAAGTCACTAAGCTCAAGTGCTTGGATGAAAGGACAGCGTGGATAAAAAGGTTTTTAAAACATGGATGTTAAGGCTGTTTTGCTTGGAGAAGACTTGGGACTGGGACAGTCTTTAGATATTATTTGAAATGCTGGCACTGTCTATCTGGATCCCAGGGCTTGAACTAGGATTTGAGGAAGTCACAGGGAAGCAGATTTCAGTCTGACATTTATTCAGTGCAAGTTTTTTGGTGCTGTAGTATATGATGAAAGATGTAAAGCTGAATAAAGCATTATTTCTGCCCTAGAGTTGTTCACAGCCTAGTCAGGCATATGGATATGTAAACAATGACTGTAACGTGTTATAGATGTAAAGACAAAATAAAGGTTAAAGAGGGCATAAAGGAGCACTCAATTGCAGAGATTTGAGGACATTATTTTTATTTTGAGCTTTAAAAAGATGAATAGGTGTTCTCAGGAGGTAGGGATCTGGCTGAGAGGGAATAATCTGAGCAAAGGTATGAAACAGCCTAATGCATTAGAGAAAAAAGTTCTTTTAGTAAGGCATTTGGGGTTGGGGAAGCTAGAAAAAGAAATGGGAGCTGGTCACACAGGGCCTTGTGTGCCAGACTAAGGGGTTTGTAGTATATATTGTAGGCAGAAGAGATCCATCAACAGATTGCAAGCAAGGAAGTATGTTCACTTTAAAGTTTGAGAAAGAATAGTGTGGAAGCACGTCTCAAATTTAGACTTACTTGTTCCCCCTCTGAACCGTGAATCAGACCATTTCAGGTAGAAGTCTTCCCCGGTTTATCTGATCTACTCGGGGCCTCAGGCTTCTCAGCTGGGAAGAGAGGATGCAAGACCAGACTGAAGAACACGGTTGAGTCCCCAGAACCAAAAGGGGGCCTTTCTGCTTCTTAGCCAGCTACCTCTTCGAGTTTTTCAAATTGTGAGGGGGACCATAAAAGGATGGAAACTTTTAGATGACATTCTACAAATTATTTTTTTCTTTAAATTAAAAGAACCTAGCCAATAAGATAGAGAATGGGCATCTAAGGCATCTCAGAGCTCTCTGATGAAGCCAGGTTGTCAAAGATCATTTGCAAAAGAAGGGAAAACTGGCATGACAAAAGCTACAGAGAGGAGAGTGAAATATAGAAGTGTTTGAAATGTTCAAGCTCACAATAAGCTTAAATTTATAGAAAATGCTAAGGTTGTCAAGAAGGCTTTTTTTTTTTTCTTTTTTAAACCTGAGGGCAAAAAGGAATGGATAAAGTAGTGTAATGGATTGACAATCAGGAAGAACAGAATAACTCAGTTTTTTTTTCTCCTACAAGGAGATATGGCTGGACCAAAATAAAATGACATGAAATTGCAAAAATGAAAAT	
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	GGGGGGCTGCGCGGCCGGGTCGGTGCGCACACGAGAAGGACGCGCGGCCCCCAGCGCTCTTGGGGGCCGCCTCGGAGCATGACCCCCGCGGGCCAGCGCCGCGCGCCTGATCCGAGGAGACCCCGCGCTCCCGCAGCCATGGGCACCGGGGGCCGGCGGGGGGCGGCGGCCGCGCCGCTGCTGGTGGCGGTGGCCGCGCTGCTACTGGGCGCCGCGGGCCACCTGTACCCCGGAGAGGTGTGTCCCGGCATGGATATCCGGAACAACCTCACTAGGTTGCATGAGCTGGAGAATTGCTCTGTCATCGAAGGACACTTGCAGATACTCTTGATGTTCAAAACGAGGCCCGAAGATTTCCGAGACCTCAGTTTCCCCAAACTCATCATGATCACTGATTACTTGCTGCTCTTCCGGGTCTATGGGCTCGAGAGCCTGAAGGACCTGTTCCCCAACCTCACGGTCATCCGGGGATCACGACTGTTCTTTAACTACGCGCTGGTCATCTTCGAGATGGTTCACCTCAAGGAACTCGGCCTCTACAACCTGATGAACATCACCCGGGGTTCTGTCCGCATCGAGAAGAACAATGAGCTCTGTTACTTGGCCACTATCGACTGGTCCCGTATCCTGGATTCCGTGGAGGATAATCACATCGTGTTGAACAAAGATGACAACGAGGAGTGTGGAGACATCTGTCCGGGTACCGCGAAGGGCAAGACCAACTGCCCCGCCACCGTCATCAACGGGCAGTTTGTCGAACGATGTTGGACTCATAGTCACTGCCAGAAAGTTTGCCCGACCATCTGTAAGTCACACGGCTGCACCGCCGAAGGCCTCTGTTGCCACAGCGAGTGCCTGGGCAACTGTTCTCAGCCCGACGACCCCACCAAGTGCGTGGCCTGCCGCAACTTCTACCTGGACGGCAGGTGTGTGGAGACCTGCCCGCCCCCGTACTACCACTTCCAGGACTGGCGCTGTGTGAACTTCAGCTTCTGCCAGGACCTGCACCACAAATGCAAGAACTCGCGGAGGCAGGGCTGCCACCAATACGTCATTCACAACAACAAGTGCATCCCTGAGTGTCCCTCCGGGTACACGATGAATTCCAGCAACTTGCTGTGCACCCCATGCCTGGGTCCCTGTCCCAAGGTGTGCCACCTCCTAGAAGGCGAGAAGACCATCGACTCGGTGACGTCTGCCCAGGAGCTCCGAGGATGCACCGTCATCAACGGGAGTCTGATCATCAACATTCGAGGAGGCAACAATCTGGCAGCTGAGCTAGAAGCCAACCTCGGCCTCATTGAAGAAATTTCAGGGTATCTAAAAATCCGCCGATCCTACGCTCTGGTGTCACTTTCCTTCTTCCGGAAGTTACGTCTGATTCGAGGAGAGACCTTGGAAATTGGGAACTACTCCTTCTATGCCTTGGACAACCAGAACCTAAGGCAGCTCTGGGACTGGAGCAAACACAACCTCACCACCACTCAGGGGAAACTCTTCTTCCACTATAACCCCAAACTCTGCTTGTCAGAAATCCACAAGATGGAAGAAGTTTCAGGAACCAAGGGGCGCCAGGAGAGAAACGACATTGCCCTGAAGACCAATGGGGACAAGGCATCCTGTGAAAATGAGTTACTTAAATTTTCTTACATTCGGACATCTTTTGACAAGATCTTGCTGAGATGGGAGCCGTACTGGCCCCCCGACTTCCGAGACCTCTTGGGGTTCATGCTGTTCTACAAAGAGGCCCCTTATCAGAATGTGACGGAGTTCGATGGGCAGGATGCGTGTGGTTCCAACAGTTGGACGGTGGTAGACATTGACCCACCCCTGAGGTCCAACGACCCCAAATCACAGAACCACCCAGGGTGGCTGATGCGGGGTCTCAAGCCCTGGACCCAGTATGCCATCTTTGTGAAGACCCTGGTCACCTTTTCGGATGAACGCCGGACCTATGGGGCCAAGAGTGACATCATTTATGTCCAGACAGATGCCACCAACCCCTCTGTGCCCCTGGATCCAATCTCAGTGTCTAACTCATCATCCCAGATTATTCTGAAGTGGAAACCACCCTCCGACCCCAATGGCAACATCACCCACTACCTGGTTTTCTGGGAGAGGCAGGCGGAAGACAGTGAGCTGTTCGAGCTGGATTATTGCCTCAAAGGGCTGAAGCTGCCCTCGAGGACCTGGTCTCCACCATTCGAGTCTGAAGATTCTCAGAAGCACAACCAGAGTGAGTATGAGGATTCGGCCGGCGAATGCTGCTCCTGTCCAAAGACAGACTCTCAGATCCTGAAGGAGCTGGAGGAGTCCTCGTTTAGGAAGACGTTTGAGGATTACCTGCACAACGTGGTTTTCGTCCCCAGAAAAACCTCTTCAGGCACTGGTGCCGAGGACCCTAGGCCATCTCGGAAACGCAGGTCCCTTGGCGATGTTGGGAATGTGACGGTGGCCGTGCCCACGGTGGCAGCTTTCCCCAACACTTCCTCGACCAGCGTGCCCACGAGTCCGGAGGAGCACAGGCCTTTTGAGAAGGTGGTGAACAAGGAGTCGCTGGTCATCTCCGGCTTGCGACACTTCACGGGCTATCGCATCGAGCTGCAGGCTTGCAACCAGGACACCCCTGAGGAACGGTGCAGTGTGGCAGCCTACGTCAGTGCGAGGACCATGCCTGAAGCCAAGGCTGATGACATTGTTGGCCCTGTGACGCATGAAATCTTTGAGAACAACGTCGTCCACTTGATGTGGCAGGAGCCGAAGGAGCCCAATGGTCTGATCGTGCTGTATGAAGTGAGTTATCGGCGATATGGTGATGAGGAGCTGCATCTCTGCGTCTCCCGCAAGCACTTCGCTCTGGAACGGGGCTGCAGGCTGCGTGGGCTGTCACCGGGGAACTACAGCGTGCGAATCCGGGCCACCTCCCTTGCGGGCAACGGCTCTTGGACGGAACCCACCTATTTCTACGTGACAGACTATTTAGACGTCCCGTCAAATATTGCAAAAATTATCATCGGCCCCCTCATCTTTGTCTTTCTCTTCAGTGTTGTGATTGGAAGTATTTATCTATTCCTGAGAAAGAGGCAGCCAGATGGGCCGCTGGGACCGCTTTACGCTTCTTCAAACCCTGAGTATCTCAGTGCCAGTGATGTGTTTCCATGCTCTGTGTACGTGCCGGACGAGTGGGAGGTGTCTCGAGAGAAGATCACCCTCCTTCGAGAGCTGGGGCAGGGCTCCTTCGGCATGGTGTATGAGGGCAATGCCAGGGACATCATCAAGGGTGAGGCAGAGACCCGCGTGGCGGTGAAGACGGTCAACGAGTCAGCCAGTCTCCGAGAGCGGATTGAGTTCCTCAATGAGGCCTCGGTCATGAAGGGCTTCACCTGCCATCACGTGGTGCGCCTCCTGGGAGTGGTGTCCAAGGGCCAGCCCACGCTGGTGGTGATGGAGCTGATGGCTCACGGAGACCTGAAGAGCTACCTCCGTTCTCTGCGGCCAGAGGCTGAGAATAATCCTGGCCGCCCTCCCCCTACCCTTCAAGAGATGATTCAGATGGCGGCAGAGATTGCTGACGGGATGGCCTACCTGAACGCCAAGAAGTTTGTGCATCGGGACCTGGCAGCGAGAAACTGCATGGTCGCCCATGATTTTACTGTCAAAATTGGAGACTTTGGAATGACCAGAGACATCTATGAAACGGATTACTACCGGAAAGGGGGCAAGGGTCTGCTCCCTGTACGGTGGATGGCACCGGAGTCCCTGAAGGATGGGGTCTTCACCACTTCTTCTGACATGTGGTCCTTTGGCGTGGTCCTTTGGGAAATCACCAGCTTGGCAGAACAGCCTTACCAAGGCCTGTCTAATGAACAGGTGTTGAAATTTGTCATGGATGGAGGGTATCTGGATCAACCCGACAACTGTCCAGAGAGAGTCACTGACCTCATGCGCATGTGCTGGCAATTCAACCCCAAGATGAGGCCAACCTTCCTGGAGATTGTCAACCTGCTCAAGGACGACCTGCACCCCAGCTTTCCAGAGGTGTCGTTCTTCCACAGCGAGGAGAACAAGGCTCCCGAGAGTGAGGAGCTGGAGATGGAGTTTGAGGACATGGAGAATGTGCCCCTGGACCGTTCCTCGCACTGTCAGAGGGAGGAGGCGGGGGGCCGGGATGGAGGGTCCTCGCTGGGTTTCAAGCGGAGCTACGAGGAACACATCCCTTACACACACATGAACGGAGGCAAGAAAAACGGGCGGATTCTGACCTTGCCTCGGTCCAATCCTTCCTAACAGTGCCTACCGTGGCGGGGGCGGGCAGGGGTTCCCATTTTCGCTTTCCTCTGGTTTGAAAGCCTCTGGAAAACTCAGGATTCTCACGACTCTACCATGTCCAGTGGAGTTCAGAGATCGTTCCTATACATTTCTGTTCATCTTAAGGTGGACTCGTTTGGTTACCAATTTAACTAGTCCTGCAGAGGATTTAACTGTGAACCTGGAGGGCAAGGGGTTTCCACAGTTGCTGCTCCTTTGGGGCAACGACGGTTTCAAACCAGGATTTTGTGTTTTTTCGTTCCCCCCACCCGCCCCCAGCAGATGGAAAGAAAGCACCTGTTTTTACAAATTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTGCTGGTGTCTGAGCTTCAGTATAAAAGACAAAACTTCCTGTTTGTGGAACAAAATTTCGAAAGAAAAAACCAAA	
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	CCAGCTGGAGCCCTGAGTGGCTGAGCTCAGGCCTTCGCAGCATTCTTGGGTGGGAGCAGCCACGGGTCAGCCACAAGGGCCACAGCCATGAATGGCACAGAAGGCCCTAACTTCTACGTGCCCTTCTCCAATGCGACGGGTGTGGTACGCAGCCCCTTCGAGTACCCACAGTACTACCTGGCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTTCTGCTGATCGTGCTGGGCTTCCCCATCAACTTCCTCACGCTCTACGTCACCGTCCAGCACAAGAAGCTGCGCACGCCTCTCAACTACATCCTGCTCAACCTAGCCGTGGCTGACCTCTTCATGGTCCTAGGTGGCTTCACCAGCACCCTCTACACCTCTCTGCATGGATACTTCGTCTTCGGGCCCACAGGATGCAATTTGGAGGGCTTCTTTGCCACCCTGGGCGGTGAAATTGCCCTGTGGTCCTTGGTGGTCCTGGCCATCGAGCGGTACGTGGTGGTGTGTAAGCCCATGAGCAACTTCCGCTTCGGGGAGAACCATGCCATCATGGGCGTTGCCTTCACCTGGGTCATGGCGCTGGCCTGCGCCGCACCCCCACTCGCCGGCTGGTCCAGGTACATCCCCGAGGGCCTGCAGTGCTCGTGTGGAATCGACTACTACACGCTCAAGCCGGAGGTCAACAACGAGTCTTTTGTCATCTACATGTTCGTGGTCCACTTCACCATCCCCATGATTATCATCTTTTTCTGCTATGGGCAGCTCGTCTTCACCGTCAAGGAGGCCGCTGCCCAGCAGCAGGAGTCAGCCACCACACAGAAGGCAGAGAAGGAGGTCACCCGCATGGTCATCATCATGGTCATCGCTTTCCTGATCTGCTGGGTGCCCTACGCCAGCGTGGCATTCTACATCTTCACCCACCAGGGCTCCAACTTCGGTCCCATCTTCATGACCATCCCAGCGTTCTTTGCCAAGAGCGCCGCCATCTACAACCCTGTCATCTATATCATGATGAACAAGCAGTTCCGGAACTGCATGCTCACCACCATCTGCTGCGGCAAGAACCCACTGGGTGACGATGAGGCCTCTGCTACCGTGTCCAAGACGGAGACGAGCCAGGTGGCCCCGGCCTAAGACCTGCCTAGGACTCTGTGGCCGACTATAGGCGTCTCCCATCCCCTACACCTTCCCCCAGCCACAGCCATCCCACCAG	
diff -r 000000000000 -r 1f08834f987e test-data/fx2tab_output4.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fx2tab_output4.tabular	Tue Mar 26 21:49:37 2024 +0000
@@ -0,0 +1,4 @@
+#id	length	GC	GC-Skew	alphabet	avg.qual	seq.hash
+ENA|AB011145|AB011145.1	4796	38.47	11.65	ACGT	0.00	c19cf05cadbdbc26e22efc2201acfcec
+ENA|M10051|M10051.1	4723	55.24	0.50	ACGT	0.00	4f6bbf79e427ef90b6f31de5023ad241
+ENA|BC112106|BC112106.1	1213	58.78	-15.01	ACGT	0.00	3b099f7df389373bb7e3269efc819599
diff -r 000000000000 -r 1f08834f987e test-data/input1.fasta.gz
Binary file test-data/input1.fasta.gz has changed
diff -r 000000000000 -r 1f08834f987e test-data/input1.fastq.gz
Binary file test-data/input1.fastq.gz has changed
diff -r 000000000000 -r 1f08834f987e test-data/locate_output1.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/locate_output1.tabular	Tue Mar 26 21:49:37 2024 +0000
@@ -0,0 +1,95 @@
+seqID	patternName	pattern	strand	start	end	matched
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	251	256	ATAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	435	440	AGAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	660	665	ATAGAG
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	741	746	AAAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	852	857	ATAAAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	1142	1147	AAAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	1320	1325	ATAGGT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	1621	1626	ATAAAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	1778	1783	AGAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	1784	1789	ATACAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	1810	1815	ATAAAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	2038	2043	ATGGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	2120	2125	CTAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	2235	2240	ATAGTT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	2243	2248	ATAAAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	2318	2323	CTAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	2527	2532	ATAAAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	2549	2554	AAAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	2603	2608	ATATAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	2651	2656	ATGGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	2726	2731	ATAGTT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	2744	2749	ATAAAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	2902	2907	TTAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	3041	3046	AAAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	3488	3493	ATGGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	3539	3544	TTAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	3675	3680	AAAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	3739	3744	ATGGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	3770	3775	ATAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	3825	3830	AGAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	3862	3867	AAAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	3870	3875	ATAGGT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	4052	4057	ATATAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	4068	4073	AGAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	4080	4085	ACAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	4388	4393	TTAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	4446	4451	ATAGAG
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	4500	4505	AAAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	4563	4568	ATAGAA
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	4607	4612	ATAGAA
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	4675	4680	ATGGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	4692	4697	ATGGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	4603	4608	ATAAAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	4459	4464	TTAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	4223	4228	GTAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	4072	4077	ATGGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	4052	4057	ATATAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	3634	3639	ATAAAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	3566	3571	ATAGAC
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	2918	2923	ACAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	2778	2783	ATACAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	2709	2714	ATAAAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	2644	2649	ATAAAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	2603	2608	ATATAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	2531	2536	ATTGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	1734	1739	ATTGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	1601	1606	ACAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	1438	1443	ATAGAA
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	1422	1427	ATAGGT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	1329	1334	ATAGAG
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	1146	1151	ATACAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	1121	1126	ATACAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	811	816	ATAGCT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	764	769	GTAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	656	661	ATAGTT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	+	250	255	ATGGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	+	664	669	AAAGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	+	1987	1992	ACAGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	+	3540	3545	AGAGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	+	3561	3566	AGAGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	+	3886	3891	ATGGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	+	4400	4405	AGAGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	+	4413	4418	ATACAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	3688	3693	ATAGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	3065	3070	ATAGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	3061	3066	ATAAAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	3025	3030	AAAGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	2956	2961	ATAGGT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	2828	2833	AGAGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	2719	2724	AAAGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	1975	1980	ATAAAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	1951	1956	ATAGGT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	1909	1914	AAAGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	1659	1664	AAAGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	1417	1422	ATAGAA
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	1319	1324	TTAGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	802	807	ACAGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	691	696	ACAGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	415	420	ATAGAC
+ENA|BC112106|BC112106.1	ATAGAT	ATAGAT	+	386	391	ATGGAT
+ENA|BC112106|BC112106.1	ATAGAT	ATAGAT	-	1000	1005	ATAGAT
+ENA|BC112106|BC112106.1	ATAGAT	ATAGAT	-	985	990	GTAGAT
+ENA|BC112106|BC112106.1	ATAGAT	ATAGAT	-	742	747	AAAGAT
+ENA|BC112106|BC112106.1	ATAGAT	ATAGAT	-	700	705	GTAGAT
diff -r 000000000000 -r 1f08834f987e test-data/locate_output2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/locate_output2.bed	Tue Mar 26 21:49:37 2024 +0000
@@ -0,0 +1,202 @@
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	136	139	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	174	177	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	254	257	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	269	272	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	275	278	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	296	299	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	322	325	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	353	356	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	377	380	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	479	482	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	484	487	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	487	490	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	490	493	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	692	695	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	695	698	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	725	728	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	796	799	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	814	817	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	827	830	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	855	858	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	890	893	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	940	943	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	977	980	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1028	1031	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1120	1123	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1124	1127	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1145	1148	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1220	1223	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1265	1268	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1346	1349	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1441	1444	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1510	1513	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1629	1632	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1693	1696	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1709	1712	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1730	1733	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1866	1869	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1902	1905	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1972	1975	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1991	1994	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2028	2031	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2037	2040	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2041	2044	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2060	2063	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2123	2126	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2147	2150	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2294	2297	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2358	2361	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2578	2581	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2590	2593	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2597	2600	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2606	2609	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2650	2653	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2661	2664	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2701	2704	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2705	2708	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2747	2750	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2777	2780	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2811	2814	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2875	2878	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2889	2892	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2908	2911	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2933	2936	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2981	2984	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3093	3096	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3125	3128	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3135	3138	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3191	3194	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3278	3281	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3342	3345	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3346	3349	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3451	3454	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3487	3490	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3491	3494	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3554	3557	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3668	3671	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3671	3674	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3678	3681	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3738	3741	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3744	3747	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3753	3756	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3773	3776	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3865	3868	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3925	3928	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3938	3941	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4000	4003	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4100	4103	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4262	4265	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4377	4380	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4391	4394	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4452	4455	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4483	4486	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4531	4534	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4577	4580	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4613	4616	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4674	4677	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4691	4694	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4750	4753	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4769	4772	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4774	4777	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4788	4791	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4794	4797	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	78	81	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	138	141	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	249	252	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	280	283	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	330	333	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	384	387	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	418	421	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	510	513	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	546	549	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	586	589	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	667	670	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	761	764	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1013	1016	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1098	1101	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1127	1130	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1214	1217	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1420	1423	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1542	1545	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1603	1606	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1627	1630	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1682	1685	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1728	1731	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1759	1762	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1774	1777	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1783	1786	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1875	1878	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1903	1906	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1939	1942	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1954	1957	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1978	1981	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1990	1993	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	2083	2086	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	2242	2245	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	2261	2264	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	2434	2437	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	2443	2446	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	2670	2673	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	2689	2692	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	2713	2716	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	2745	2748	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	2770	2773	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	2788	2791	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	2809	2812	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	2815	2818	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3091	3094	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3148	3151	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3158	3161	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3243	3246	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3250	3253	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3259	3262	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3355	3358	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3369	3372	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3444	3447	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3453	3456	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3543	3546	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3552	3555	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3576	3579	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3633	3636	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3643	3646	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3675	3678	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3691	3694	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3744	3747	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3766	3769	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3792	3795	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3862	3865	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3885	3888	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3889	3892	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3942	3945	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3948	3951	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3972	3975	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	4092	4095	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	4107	4110	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	4114	4117	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	4168	4171	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	4227	4230	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	4383	4386	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	4590	4593	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	87	90	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	91	94	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	130	133	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	188	191	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	201	204	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	216	219	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	342	345	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	385	388	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	413	416	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	513	516	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	541	544	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	549	552	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	573	576	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	705	708	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	732	735	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	754	757	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	843	846	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	855	858	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	948	951	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	1008	1011	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	1011	1014	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	1035	1038	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	1078	1081	A[TU]G	0	+
diff -r 000000000000 -r 1f08834f987e test-data/locate_output3.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/locate_output3.gtf	Tue Mar 26 21:49:37 2024 +0000
@@ -0,0 +1,4 @@
+ENA|AB011145|AB011145.1	SeqKit	location	2270	2276	0	+	.	gene_id "test_motif2"; 
+ENA|AB011145|AB011145.1	SeqKit	location	2642	2648	0	+	.	gene_id "test_motif2"; 
+ENA|AB011145|AB011145.1	SeqKit	location	2655	2661	0	+	.	gene_id "test_motif2"; 
+ENA|AB011145|AB011145.1	SeqKit	location	2771	2777	0	+	.	gene_id "test_motif2"; 
diff -r 000000000000 -r 1f08834f987e test-data/motif_sequence.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_sequence.fasta	Tue Mar 26 21:49:37 2024 +0000
@@ -0,0 +1,4 @@
+>test_motif
+ATATACTAT
+>test_motif2
+ATATTTA
diff -r 000000000000 -r 1f08834f987e test-data/sort_output1.fastq.gz
Binary file test-data/sort_output1.fastq.gz has changed
diff -r 000000000000 -r 1f08834f987e test-data/sort_output2.fasta.gz
Binary file test-data/sort_output2.fasta.gz has changed
diff -r 000000000000 -r 1f08834f987e test-data/sort_output3.fasta.gz
Binary file test-data/sort_output3.fasta.gz has changed
diff -r 000000000000 -r 1f08834f987e test-data/sort_output4.fasta.gz
Binary file test-data/sort_output4.fasta.gz has changed
diff -r 000000000000 -r 1f08834f987e test-data/sort_output5.fastq.gz
Binary file test-data/sort_output5.fastq.gz has changed
diff -r 000000000000 -r 1f08834f987e test-data/sort_output6.fastq.gz
Binary file test-data/sort_output6.fastq.gz has changed
diff -r 000000000000 -r 1f08834f987e test-data/stats_output1.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stats_output1.tabular	Tue Mar 26 21:49:37 2024 +0000
@@ -0,0 +1,2 @@
+file	format	type	num_seqs	sum_len	min_len	avg_len	max_len	Q1	Q2	Q3	sum_gap	N50	Q20(%)	Q30(%)	GC(%)
+input1_fastq_gz	FASTQ	DNA	5	505	101	101.0	101	50.5	101.0	50.5	0	101	98.02	89.31	35.45
diff -r 000000000000 -r 1f08834f987e test-data/stats_output2.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stats_output2.tabular	Tue Mar 26 21:49:37 2024 +0000
@@ -0,0 +1,2 @@
+file	format	type	num_seqs	sum_len	min_len	avg_len	max_len	Q1	Q2	Q3	sum_gap	N50	Q20(%)	Q30(%)	GC(%)
+input1_fasta_gz	FASTA	DNA	3	10732	1213	3577.3	4796	2968.0	4723.0	4759.5	0	4723	0.00	0.00	48.15