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changeset 0:91ebd197998b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
author iuc
date Mon, 12 May 2025 18:06:27 +0000
parents
children ffd1e2652813
files macros.xml samtools_faidx.xml test-data/out.tabular test-data/samtools_fastx-out1-2.fasta
diffstat 4 files changed, 868 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon May 12 18:06:27 2025 +0000
@@ -0,0 +1,233 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">samtools</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <!-- NOTE: for some tools only the version of the requirement but not the
+        tool's version is controlled by the TOOL_VERSION token 
+        (because their version is ahead of the requirement version .. 
+         please only bump the minor version in order to let the requirement
+         version catch up eventually). To find the tools check:
+        `grep "<tool" . -r | grep -v VERSION_SUFFIX | cut -d":" -f 1` -->
+    <token name="@TOOL_VERSION@">1.20</token>
+    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@PROFILE@">22.05</token>
+    <token name="@FLAGS@"><![CDATA[
+        #set $flags = 0
+        #if $filter
+            #set $flags = sum(map(int, str($filter).split(',')))
+        #end if
+    ]]></token>
+    <token name="@PREPARE_IDX@"><![CDATA[
+        ##prepare input and indices
+        ln -s '$input' infile &&
+        #if $input.is_of_type('bam'):
+            #if str( $input.metadata.bam_index ) != "None":
+                ln -s '${input.metadata.bam_index}' infile.bai &&
+            #else:
+                samtools index infile infile.bai &&
+            #end if
+        #elif $input.is_of_type('cram'):
+            #if str( $input.metadata.cram_index ) != "None":
+                ln -s '${input.metadata.cram_index}' infile.crai &&
+            #else:
+                samtools index infile infile.crai &&
+            #end if
+        #end if
+    ]]></token>
+    <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[
+        ##prepare input and indices
+        #for $i, $bam in enumerate( $input_bams ):
+            ln -s '$bam' '${i}' &&
+            #if $bam.is_of_type('bam'):
+                #if str( $bam.metadata.bam_index ) != "None":
+                    ln -s '${bam.metadata.bam_index}' '${i}.bai' &&
+                #else:
+                    samtools index '${i}' '${i}.bai' &&
+                #end if
+            #elif $bam.is_of_type('cram'):
+                #if str( $bam.metadata.cram_index ) != "None":
+                    ln -s '${bam.metadata.cram_index}' '${i}.crai' &&
+                #else:
+                    samtools index '${i}' '${i}.crai' &&
+                #end if
+            #end if
+        #end for
+    ]]></token>
+    <token name="@PREPARE_FASTA_IDX@"><![CDATA[
+        ## Make the user-selected reference genome, if any, accessible through
+        ## a shell variable $reffa, index the reference if necessary, and make
+        ## the fai-index file available through a shell variable $reffai.
+
+        ## For a cached genome simply sets the shell variables to point to the
+        ## genome file and its precalculated index.
+        ## For a genome from the user's history, if that genome is a plain
+        ## fasta file, the code creates a symlink in the pwd, creates the fai
+        ## index file next to it, then sets the shell variables to point to the
+        ## symlink and its index.
+        ## For a fasta.gz dataset from the user's history, it tries the same,
+        ## but this will only succeed if the file got compressed with bgzip.
+        ## For a regular gzipped file samtools faidx will fail, in which case
+        ## the code falls back to decompressing to plain fasta before
+        ## reattempting the indexing.
+        ## Indexing of a bgzipped file produces a regular fai index file *and*
+        ## a compressed gzi file. The former is identical to the fai index of
+        ## the uncompressed fasta.
+
+        ## If the user has not selected a reference (it's an optional parameter
+        ## in some samtools wrappers), a cheetah boolean use_ref is set to
+        ## False to encode that fact.
+
+        #set use_ref=True
+        #if $addref_cond.addref_select == "history":
+            #if $addref_cond.ref.is_of_type('fasta'):
+                reffa="reference.fa" &&
+                ln -s '${addref_cond.ref}' \$reffa &&
+                samtools faidx \$reffa &&
+            #else:
+                reffa="reference.fa.gz" &&
+                ln -s '${addref_cond.ref}' \$reffa &&
+                {
+                    samtools faidx \$reffa ||
+                    {
+                        echo "Failed to index compressed reference. Trying decompressed ..." 1>&2 &&
+                        gzip -dc \$reffa > reference.fa &&
+                        reffa="reference.fa" &&
+                        samtools faidx \$reffa;
+                    }
+                } &&
+            #end if
+            reffai=\$reffa.fai &&
+        #elif $addref_cond.addref_select == "cached":
+            ## in case of cached the absolute path is used which allows to read 
+            ## a cram file  without specifying the reference
+            reffa='${addref_cond.ref.fields.path}' &&
+            reffai=\$reffa.fai &&
+        #else
+            #set use_ref=False
+        #end if
+    ]]></token>
+
+    <xml name="optional_reference" token_help="" token_argument="">
+        <conditional name="addref_cond">
+            <param name="addref_select" type="select" label="Use a reference sequence">
+                <help>@HELP@</help>
+                <option value="no">No</option>
+                <option value="history">Use a genome/index from the history</option>
+                <option value="cached">Use a built-in genome</option>
+            </param>
+            <when value="no"/>
+            <when value="history">
+                <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/>
+            </when>
+            <when value="cached">
+                <param name="ref" argument="@ARGUMENT@" type="select" label="Reference">
+                    <options from_data_table="fasta_indexes">
+                        <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/>
+                    </options>
+                    <validator  type="no_options" message="No reference genome is available for the build associated with the selected input dataset"/>
+                </param>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="mandatory_reference" token_help="" token_argument="">
+        <conditional name="addref_cond">
+            <param name="addref_select" type="select" label="Use a reference sequence">
+                <help>@HELP@</help>
+                <option value="history">Use a genome/index from the history</option>
+                <option value="cached">Use a built-in genome</option>
+            </param>
+            <when value="history">
+                <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/>
+            </when>
+            <when value="cached">
+                <param name="ref" argument="@ARGUMENT@" type="select" label="Reference">
+                    <options from_data_table="fasta_indexes">
+                        <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/>
+                        <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
+                    </options>
+                </param>
+            </when>
+        </conditional>
+    </xml>
+
+
+    <token name="@ADDTHREADS@"><![CDATA[
+        ##compute the number of ADDITIONAL threads to be used by samtools (-@)
+        addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
+    ]]></token>
+    <token name="@ADDMEMORY@"><![CDATA[
+        ##compute the number of memory available to samtools sort (-m)
+        ##use only 75% of available: https://github.com/samtools/samtools/issues/831
+        addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} &&
+        ((addmemory=addmemory*75/100)) &&
+    ]]></token>
+    <xml name="seed_input">
+       <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." />
+    </xml>
+    <xml name="flag_options" token_s1="false" token_s2="false" token_s4="false" token_s8="false" token_s16="false" token_s32="false" token_s64="false" token_s128="false" token_s256="false" token_s512="false" token_s1024="false" token_s2048="false">
+        <option value="1" selected="@S1@">Read is paired</option>
+        <option value="2" selected="@S2@">Read is mapped in a proper pair</option>
+        <option value="4" selected="@S4@">Read is unmapped</option>
+        <option value="8" selected="@S8@">Mate is unmapped</option>
+        <option value="16" selected="@S16@">Read is mapped to the reverse strand of the reference</option>
+        <option value="32" selected="@S32@">Mate is mapped to the reverse strand of the reference</option>
+        <option value="64" selected="@S64@">Read is the first in a pair</option>
+        <option value="128" selected="@S128@">Read is the second in a pair</option>
+        <option value="256" selected="@S256@">Alignment of the read is not primary</option>
+        <option value="512" selected="@S512@">Read fails platform/vendor quality checks</option>
+        <option value="1024" selected="@S1024@">Read is a PCR or optical duplicate</option>
+        <option value="2048" selected="@S2048@">Alignment is supplementary</option>
+    </xml>
+
+    <!-- region specification macros and tokens for tools that allow the specification
+         of region by bed file / space separated list of regions -->
+    <token name="@REGIONS_FILE@"><![CDATA[
+        #if $cond_region.select_region == 'tab':
+            -t '$cond_region.targetregions'
+        #end if
+    ]]></token>
+    <token name="@REGIONS_MANUAL@"><![CDATA[
+        #if $cond_region.select_region == 'text':
+            #for $i, $x in enumerate($cond_region.regions_repeat):
+               '${x.region}'
+            #end for
+        #end if
+    ]]></token>
+    <xml name="regions_macro">
+        <conditional name="cond_region">
+            <param name="select_region" type="select" label="Filter by regions" help="restricts output to only those alignments which overlap the specified region(s)">
+                <option value="no" selected="True">No</option>
+                <option value="text">Manualy specify regions</option>
+                <option value="tab">Regions from tabular file</option>
+            </param>
+            <when value="no"/>
+            <when value="text">
+                <repeat name="regions_repeat" min="1" default="1" title="Regions">
+                    <param name="region" type="text" label="region" help="format chr:from-to">
+                        <validator type="regex" message="Required format: CHR[:FROM[-TO]]; where CHR: string containing any character except quotes, whitespace and colon; FROM and TO: any integer">^[^\s'\":]+(:\d+(-\d+){0,1}){0,1}$</validator>
+                    </param>
+                </repeat>
+            </when>
+            <when value="tab">
+                <param name="targetregions" argument="-t/--target-regions" type="data" format="tabular" label="Target regions file" help="Do stats in these regions only. Tab-delimited file chr,from,to (1-based, inclusive)" />
+            </when>
+        </conditional>
+    </xml>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/gigascience/giab008</citation>
+        </citations>
+    </xml>
+    <xml name="version_command">
+        <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:" level="fatal" description="Error" />
+        </stdio>
+    </xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_faidx.xml	Mon May 12 18:06:27 2025 +0000
@@ -0,0 +1,35 @@
+<tool id="samtools_faidx" name="Samtools faidx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Index a FASTA file</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+    samtools
+        faidx
+        '$in_fasta'
+        --fai-idx '$output'
+    ]]></command>
+    <inputs>
+        <param name="in_fasta" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz" label="dataset with sequences" />
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="in_fasta" value="samtools_fastx-out1-2.fasta" />
+            <output name="output" file="out.tabular" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+Runs the ``samtools faidx`` command to index reference sequence in the FASTA format reference sequence.
+
+Full `documentation <https://www.htslib.org/doc/samtools-faidx.html>`_ for the faidx command.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out.tabular	Mon May 12 18:06:27 2025 +0000
@@ -0,0 +1,200 @@
+chrM_101_581_3:0:0_1:0:0_45	70	29	70	71
+chrM_317_794_1:3:0_0:1:0_18	70	129	70	71
+chrM_424_929_1:0:1_1:1:0_4a	70	229	70	71
+chrM_296_703_3:1:0_0:1:0_b	70	328	70	71
+chrM_271_788_1:2:0_0:1:0_73	70	428	70	71
+chrM_1166_1638_1:0:0_3:1:0_54	70	530	70	71
+chrM_1187_1670_2:0:0_1:1:0_5	70	631	70	71
+chrM_826_1305_2:0:0_0:0:0_63	70	732	70	71
+chrM_769_1311_4:2:0_1:0:0_9b	70	833	70	71
+chrM_946_1374_2:0:1_1:0:0_b7	70	934	70	71
+chrM_1461_2059_1:2:0_0:0:0_8f	70	1036	70	71
+chrM_1366_1837_1:0:0_0:0:0_24	70	1138	70	71
+chrM_1396_1891_4:1:0_3:0:0_55	70	1240	70	71
+chrM_1654_2097_0:1:0_1:0:0_a8	70	1342	70	71
+chrM_2195_2667_1:0:0_2:0:0_95	70	1444	70	71
+chrM_1772_2275_1:0:0_1:0:0_3f	70	1546	70	71
+chrM_2021_2595_3:0:0_2:0:0_22	70	1648	70	71
+chrM_2706_3137_0:1:0_1:0:1_af	70	1750	70	71
+chrM_2789_3314_1:0:0_0:1:0_f	70	1851	70	71
+chrM_2674_3159_3:1:0_1:1:1_e	70	1952	70	71
+chrM_3103_3621_2:1:0_1:0:0_71	70	2054	70	71
+chrM_3169_3659_1:2:0_2:0:0_68	70	2156	70	71
+chrM_2740_3253_1:1:0_1:1:0_6c	70	2258	70	71
+chrM_3187_3702_2:1:0_1:1:0_8d	70	2360	70	71
+chrM_3204_3728_0:1:0_2:2:0_4b	70	2462	70	71
+chrM_2945_3338_1:0:0_1:1:0_19	70	2564	70	71
+chrM_3289_3819_1:1:0_4:1:0_3c	70	2666	70	71
+chrM_3504_4052_0:0:0_0:2:0_b9	70	2768	70	71
+chrM_3542_4113_1:0:0_0:0:0_65	70	2870	70	71
+chrM_3560_4153_2:0:0_1:0:0_4f	70	2972	70	71
+chrM_3562_4117_0:0:0_3:0:0_51	70	3074	70	71
+chrM_3135_3669_1:2:0_1:0:0_2c	70	3176	70	71
+chrM_3422_3872_1:0:0_2:1:0_3b	70	3278	70	71
+chrM_3587_4003_0:0:0_1:1:0_a7	70	3380	70	71
+chrM_3998_4489_2:1:0_1:1:0_be	70	3482	70	71
+chrM_4007_4449_2:0:0_3:1:0_17	70	3584	70	71
+chrM_4139_4621_1:0:0_4:0:0_7e	70	3686	70	71
+chrM_4200_4733_4:0:0_0:1:0_6f	70	3788	70	71
+chrM_3799_4278_3:2:0_1:0:0_1d	70	3890	70	71
+chrM_4256_4777_1:0:0_2:2:0_66	70	3992	70	71
+chrM_3889_4361_3:0:0_3:0:0_33	70	4094	70	71
+chrM_3912_4414_3:0:0_2:1:0_91	70	4196	70	71
+chrM_3945_4422_1:2:0_0:1:0_64	70	4298	70	71
+chrM_4354_4860_0:1:0_1:0:1_b1	70	4400	70	71
+chrM_4383_4859_1:1:0_0:0:1_90	70	4502	70	71
+chrM_4425_4987_2:0:0_2:3:0_35	70	4604	70	71
+chrM_4427_4991_1:0:0_3:3:0_7	70	4705	70	71
+chrM_4480_4986_1:1:0_2:3:0_98	70	4807	70	71
+chrM_4491_4937_1:0:0_1:1:0_5e	70	4909	70	71
+chrM_4079_4594_1:0:0_3:0:0_28	70	5011	70	71
+chrM_4140_4598_2:0:0_2:0:0_12	70	5113	70	71
+chrM_4627_5166_2:0:0_2:1:0_13	70	5215	70	71
+chrM_4810_5337_0:1:0_0:3:0_9c	70	5317	70	71
+chrM_4306_4893_3:0:0_3:1:0_83	70	5419	70	71
+chrM_4842_5304_1:1:0_0:2:0_41	70	5521	70	71
+chrM_4484_4978_1:2:0_1:2:0_3d	70	5623	70	71
+chrM_4918_5435_0:2:0_1:1:0_74	70	5725	70	71
+chrM_5540_5928_2:2:0_1:0:0_2d	70	5827	70	71
+chrM_5583_6032_2:0:0_3:1:0_2b	70	5929	70	71
+chrM_5645_6067_1:2:0_1:3:0_1c	70	6031	70	71
+chrM_5770_6257_3:0:0_1:2:0_46	70	6133	70	71
+chrM_5340_5854_0:1:0_0:0:0_a	70	6234	70	71
+chrM_5499_5905_2:3:0_1:0:0_2f	70	6336	70	71
+chrM_5451_5933_2:1:0_1:1:0_57	70	6438	70	71
+chrM_5403_5984_0:0:0_1:2:0_ab	70	6540	70	71
+chrM_5930_6421_2:3:0_1:1:0_2e	70	6642	70	71
+chrM_5615_6110_2:1:0_0:3:0_14	70	6744	70	71
+chrM_6074_6685_2:0:0_0:2:0_a3	70	6846	70	71
+chrM_5831_6292_0:0:0_1:0:0_15	70	6948	70	71
+chrM_6228_6791_1:0:0_0:0:0_ae	70	7050	70	71
+chrM_6246_6734_0:0:0_1:0:0_69	70	7152	70	71
+chrM_6261_6802_2:0:0_2:0:0_87	70	7254	70	71
+chrM_5910_6386_0:2:0_1:1:0_1e	70	7356	70	71
+chrM_6356_6909_2:1:0_4:0:0_72	70	7458	70	71
+chrM_6366_6887_1:1:0_3:0:0_85	70	7560	70	71
+chrM_5959_6526_0:2:0_1:2:0_c5	70	7662	70	71
+chrM_6458_6985_2:2:0_1:0:0_b5	70	7764	70	71
+chrM_6510_7029_2:1:0_1:0:0_16	70	7866	70	71
+chrM_6138_6598_0:0:0_1:2:0_6e	70	7968	70	71
+chrM_6719_7233_1:0:0_4:1:0_b0	70	8070	70	71
+chrM_6720_7201_2:1:0_1:0:0_b8	70	8172	70	71
+chrM_6367_6804_0:1:0_1:1:0_5d	70	8274	70	71
+chrM_6845_7289_0:0:0_4:0:0_5c	70	8376	70	71
+chrM_6864_7309_1:0:0_0:0:0_a6	70	8478	70	71
+chrM_6514_6987_2:1:0_1:0:0_8	70	8579	70	71
+chrM_7046_7557_1:0:0_2:2:1_c6	70	8681	70	71
+chrM_7156_7672_2:1:0_0:0:0_53	70	8783	70	71
+chrM_7258_7724_0:1:0_0:0:0_10	70	8885	70	71
+chrM_7339_7816_1:0:0_3:4:0_43	70	8987	70	71
+chrM_6938_7424_2:0:0_1:0:0_b4	70	9089	70	71
+chrM_7188_7644_1:1:0_2:1:0_a9	70	9191	70	71
+chrM_7668_8147_1:1:1_1:2:1_6b	70	9293	70	71
+chrM_7223_7762_2:1:0_1:1:0_a1	70	9395	70	71
+chrM_7358_7894_0:0:0_1:0:1_bc	70	9497	70	71
+chrM_7550_8033_2:2:0_0:0:0_26	70	9599	70	71
+chrM_7964_8497_0:0:0_2:0:0_8c	70	9701	70	71
+chrM_7785_8278_5:1:0_2:0:0_99	70	9803	70	71
+chrM_7728_8283_1:4:0_2:0:0_1b	70	9905	70	71
+chrM_7788_8291_0:0:0_3:1:0_86	70	10007	70	71
+chrM_7835_8385_1:0:1_2:0:0_c7	70	10109	70	71
+chrM_8325_8781_1:0:0_2:0:0_9d	70	10211	70	71
+chrM_7872_8415_2:0:1_1:0:0_1a	70	10313	70	71
+chrM_7939_8482_1:1:0_2:0:0_25	70	10415	70	71
+chrM_8733_9211_0:0:0_0:0:0_47	70	10517	70	71
+chrM_8419_8906_1:0:0_3:0:0_9f	70	10619	70	71
+chrM_8886_9293_2:1:0_0:0:1_a2	70	10721	70	71
+chrM_9032_9593_1:2:1_1:0:0_b2	70	10823	70	71
+chrM_8761_9187_1:1:0_0:0:0_ba	70	10925	70	71
+chrM_9120_9714_1:1:0_0:1:0_88	70	11027	70	71
+chrM_9142_9548_1:1:0_1:2:0_77	70	11129	70	71
+chrM_9150_9818_1:1:0_1:1:0_bf	70	11231	70	71
+chrM_8863_9244_0:0:0_1:0:0_92	70	11333	70	71
+chrM_8794_9257_1:1:0_1:0:0_79	70	11435	70	71
+chrM_9222_9781_2:0:1_1:0:0_23	70	11537	70	71
+chrM_9038_9471_1:3:0_1:1:0_8a	70	11639	70	71
+chrM_9031_9522_3:3:0_2:0:0_84	70	11741	70	71
+chrM_9505_10155_3:0:0_1:0:0_9a	70	11844	70	71
+chrM_9647_10116_2:0:0_1:2:0_2a	70	11947	70	71
+chrM_9409_9920_3:1:0_1:0:0_d	70	12048	70	71
+chrM_9897_10466_3:1:0_1:0:2_1	70	12150	70	71
+chrM_9907_10368_2:0:0_1:0:0_c2	70	12253	70	71
+chrM_9910_10411_1:1:0_0:1:2_bb	70	12356	70	71
+chrM_9496_9991_0:0:0_3:1:0_80	70	12458	70	71
+chrM_10106_10577_3:1:0_2:0:0_5b	70	12562	70	71
+chrM_10193_10658_0:2:0_1:0:0_b6	70	12666	70	71
+chrM_9735_10262_1:0:0_1:2:0_40	70	12769	70	71
+chrM_10206_10702_1:0:0_3:1:0_9e	70	12873	70	71
+chrM_10254_10719_0:0:0_1:1:0_8e	70	12977	70	71
+chrM_10023_10620_2:2:0_3:0:0_4	70	13080	70	71
+chrM_10203_10663_1:0:0_1:0:0_42	70	13184	70	71
+chrM_10362_10821_2:1:2_0:0:0_c	70	13287	70	71
+chrM_10389_10966_1:0:0_1:0:0_61	70	13391	70	71
+chrM_10461_11010_1:1:0_0:0:0_21	70	13495	70	71
+chrM_11041_11475_1:0:0_1:1:0_7b	70	13599	70	71
+chrM_10767_11161_1:0:0_2:0:1_39	70	13703	70	71
+chrM_11211_11625_0:1:0_2:0:0_37	70	13807	70	71
+chrM_11475_12014_1:1:0_2:1:0_56	70	13911	70	71
+chrM_11195_11669_2:0:0_1:0:0_49	70	14015	70	71
+chrM_11464_11999_0:1:0_3:1:0_3a	70	14119	70	71
+chrM_12174_12610_1:1:0_0:0:1_93	70	14223	70	71
+chrM_11715_12248_2:1:0_1:1:1_a0	70	14327	70	71
+chrM_12218_12618_2:1:1_1:1:0_32	70	14431	70	71
+chrM_12243_12713_2:0:0_1:0:0_bd	70	14535	70	71
+chrM_12113_12598_3:3:0_2:0:1_70	70	14639	70	71
+chrM_12064_12604_0:1:0_1:0:1_aa	70	14743	70	71
+chrM_12577_13079_0:0:0_1:1:1_11	70	14847	70	71
+chrM_12622_13091_0:0:0_3:0:1_78	70	14951	70	71
+chrM_12705_13147_4:0:0_2:0:0_94	70	15055	70	71
+chrM_12275_12781_1:0:0_1:0:1_6	70	15158	70	71
+chrM_12355_12806_0:1:0_1:0:0_6a	70	15262	70	71
+chrM_12440_12937_5:0:0_1:0:0_8b	70	15366	70	71
+chrM_12640_13011_2:0:0_2:1:0_62	70	15470	70	71
+chrM_12982_13475_3:1:0_2:0:1_75	70	15574	70	71
+chrM_12720_13279_1:0:1_2:0:0_2	70	15677	70	71
+chrM_12881_13337_0:0:0_1:1:0_89	70	15781	70	71
+chrM_13281_13783_1:1:0_1:0:0_67	70	15885	70	71
+chrM_13494_14044_3:1:0_1:1:0_7d	70	15989	70	71
+chrM_13142_13600_1:0:0_1:2:0_34	70	16093	70	71
+chrM_13326_13750_2:0:1_2:1:0_82	70	16197	70	71
+chrM_13198_13763_2:0:0_0:1:0_7c	70	16301	70	71
+chrM_13715_14154_1:0:0_1:1:0_96	70	16405	70	71
+chrM_13338_13860_2:1:1_2:0:1_4d	70	16509	70	71
+chrM_13813_14351_0:1:0_0:1:0_1f	70	16613	70	71
+chrM_13482_13976_0:0:0_1:2:0_c1	70	16717	70	71
+chrM_13910_14543_2:1:0_1:1:0_30	70	16821	70	71
+chrM_13936_14395_2:2:0_1:1:1_76	70	16925	70	71
+chrM_13940_14475_1:1:0_3:2:0_27	70	17029	70	71
+chrM_14052_14489_0:0:0_3:4:0_4c	70	17133	70	71
+chrM_14105_14613_0:0:0_2:0:0_48	70	17237	70	71
+chrM_14128_14614_0:1:0_1:1:0_97	70	17341	70	71
+chrM_14131_14628_2:1:0_2:1:0_36	70	17445	70	71
+chrM_13791_14330_0:0:0_3:0:0_29	70	17549	70	71
+chrM_13944_14351_1:1:0_0:0:0_44	70	17653	70	71
+chrM_13992_14451_1:1:0_1:3:0_52	70	17757	70	71
+chrM_14442_15026_1:2:0_3:0:0_60	70	17861	70	71
+chrM_14576_14894_2:0:0_0:0:0_5f	70	17965	70	71
+chrM_14707_15163_1:1:0_1:2:0_9	70	18068	70	71
+chrM_14728_15189_1:2:0_2:0:0_7a	70	18172	70	71
+chrM_14794_15314_1:0:0_1:0:0_c0	70	18276	70	71
+chrM_14975_15480_1:0:1_0:1:0_4e	70	18380	70	71
+chrM_15196_15749_1:1:1_2:1:0_c4	70	18484	70	71
+chrM_14768_15298_0:1:0_1:1:0_ac	70	18588	70	71
+chrM_14885_15311_3:1:0_1:0:0_3	70	18691	70	71
+chrM_14820_15346_1:0:0_0:0:0_5a	70	18795	70	71
+chrM_14858_15398_0:0:0_3:0:0_b3	70	18899	70	71
+chrM_15417_15889_0:0:0_2:0:0_50	70	19003	70	71
+chrM_14988_15504_0:0:0_1:1:0_38	70	19107	70	71
+chrM_15462_15945_2:1:0_0:0:0_0	70	19210	70	71
+chrM_15171_15615_1:0:0_0:1:0_c3	70	19314	70	71
+chrM_15361_15805_1:0:0_2:0:0_81	70	19418	70	71
+chrM_15481_15968_1:2:0_2:0:0_6d	70	19522	70	71
+chrM_15523_16020_2:1:0_1:1:0_31	70	19626	70	71
+chrM_15549_16044_0:1:0_1:1:0_59	70	19730	70	71
+chrM_15720_16131_0:1:0_2:1:0_58	70	19834	70	71
+chrM_15642_16224_2:1:0_0:0:0_a5	70	19938	70	71
+chrM_15820_16268_3:1:0_1:0:2_7f	70	20042	70	71
+chrM_13991_14484_3:1:0_3:4:0_20	70	20146	70	71
+chrM_8781_9305_4:1:0_3:0:1_3e	70	20248	70	71
+chrM_14312_14826_2:1:1_4:1:0_a4	70	20352	70	71
+chrM_408_812_0:2:1_4:2:0_ad	70	20452	70	71
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samtools_fastx-out1-2.fasta	Mon May 12 18:06:27 2025 +0000
@@ -0,0 +1,400 @@
+>chrM_101_581_3:0:0_1:0:0_45
+GAGGTAAAATTACACATGCAAACCTCCATAGACCGGAGAAAAATCCCTTAAAGATTTACTTAAAATTTAA
+>chrM_317_794_1:3:0_0:1:0_18
+CTCGGTCATACGATTAACCCAAACTAAATATTTTCGGCGTAAAACGTGTCATCTATAAATAAATAAATAG
+>chrM_424_929_1:0:1_1:1:0_4a
+GGACCTAAACCGTCAATAACGAAAGTAATTCTAGTCATTTATAATCCACGACAGCTAAGACCCAAACTGG
+>chrM_296_703_3:1:0_0:1:0_b
+GGGTTTGCTGAAGATGGCGGTATATAGGCTGAATTAGCAAGTGATGGTGAGGTAGAGCGGGGTTTATCGA
+>chrM_271_788_1:2:0_0:1:0_73
+TAGCCCATTTCTTCCCATTGCATTGGCTACACCTTGACCTAACGTTTTTATGTTTGATTCTTTTGCTTAC
+>chrM_1166_1638_1:0:0_3:1:0_54
+AGAATTGGAGAAAGAAATTCGTACATCTAGGAGCTATAGAACTAGTACCGCAAGGGAAAGATGAAAGACT
+>chrM_1187_1670_2:0:0_1:1:0_5
+TACATCTAGGAGCTATAGAACTAGAACCGCAAGGGAAAGATGAAAGCCTAATTAAAAGTAAGAACAAGCA
+>chrM_826_1305_2:0:0_0:0:0_63
+AGAAGTTTTCTAGTTAGTTCATTATGCAAAAGGTACAAGGTTTAATCTTTGCTTGTTCTTACTTTTAATT
+>chrM_769_1311_4:2:0_1:0:0_9b
+CAAAGGGAAGACATGGGGTACATTTTCTTATAACAGAACATTACTATCCCCTTTATGAAACTAAAGGACT
+>chrM_946_1374_2:0:1_1:0:0_b7
+GTTGATTCATAAAATTGTTTTTAGGTAGGTCGTTTGGTTTCGGGGTTTCTAGCTGTAATTCTTTTAGTTA
+>chrM_1461_2059_1:2:0_0:0:0_8f
+GAATTTAAGTTCAATTATAAACTTGCTGAAAAAAGAACAAAATCAAAAAGTAAGTTTAGATTATAGCCAA
+>chrM_1366_1837_1:0:0_0:0:0_24
+ATTTATAGTGTGATTATTGCCTATAGTCTGATTAACTAACAATGGTTATCCGAGTTGTTATACGCGTATG
+>chrM_1396_1891_4:1:0_3:0:0_55
+GAGAAGATTTTTAGGTAGAGGTGAAACGCCTACCGAGCTTGTTGATAGCTTGTTACCCAAAAAGTGAATT
+>chrM_1654_2097_0:1:0_1:0:0_a8
+AGAGACAGTTGGACCCTCGTTTAGCCGTTCATGCTAGTCCCTAATTAAGGACCAAGTGATTATGCTACCT
+>chrM_2195_2667_1:0:0_2:0:0_95
+TTTAATTTATTAAACCTAATGGCCCAAAAACTATAGTCTAAGTTTGAAATTTCGGTTGGGGTGACCTCGG
+>chrM_1772_2275_1:0:0_1:0:0_3f
+ATTTTTATTCTCCGAGGTCACCCCAACCGAAATTTCAAACTTATACTATAGTTTTTGGGCCATTAGGTTT
+>chrM_2021_2595_3:0:0_2:0:0_22
+AAGGTGGCTCTATTTCTCTTGACCTTTCGTACTGGGAGAAATCGTAAATAGATAGAAACCGACCAGGATT
+>chrM_2706_3137_0:1:0_1:0:1_af
+AGACTTAAAACCTTGTTCCCAGAGGTTCAAATCCTCTCCCTAATAGTGTTCTTTATTATTATCCTAACAC
+>chrM_2789_3314_1:0:0_0:1:0_f
+TCTAATCGCCATAGCCTTCCTCACATTAGTAGAACGCAAAATCTTAGGGTACATACAACTACGAAAAGGC
+>chrM_2674_3159_3:1:0_1:1:1_e
+CTACGGCTCGTAAAGCTCCGATTAGTGAGAATTTGGAGTTTGAGGCTCATCCTGATCAAGAATGGAGTAA
+>chrM_3103_3621_2:1:0_1:0:0_71
+GATCAGGATGATCCTCAAACTCCAAATCCTCACTAATCGGAGCTTTACGAGCCGTAGCCCAAACAATTTC
+>chrM_3169_3659_1:2:0_2:0:0_68
+TTTCATATGATGTAACCATAGCTATTATCCTTTTAACAGTTCTATTAATAAATGGATTCTACTCTCTACA
+>chrM_2740_3253_1:1:0_1:1:0_6c
+GTTGTAATAAGTGTTTTTAGAGAGTAGAATCCATTTATTAATAGAACTGATAAAAGGATAATAGCTATGG
+>chrM_3187_3702_2:1:0_1:1:0_8d
+TAGCTATTCTCCTTTTATCAGTTCTATTAATAAATGGATTCTACTCTCTACAAACACTTATTACAACCGA
+>chrM_3204_3728_0:1:0_2:2:0_4b
+TCAGTTCTATTAATAAATGGATTCTACTCTCTACAAACACTTATTACAACCCAAGAACACATATGATTAC
+>chrM_2945_3338_1:0:0_1:1:0_19
+GGCCCGGTTTGTTTCTGCTAGGGTTGAGATATATCATATTATGGCTATGGGTCAGGCTGGCAGACGTAAT
+>chrM_3289_3819_1:1:0_4:1:0_3c
+CCAAAGCCATAATATGATATATCTCAACCCTAGCAGAAACAAACCGGGCCCCCTTCGACCTGACAGAAGG
+>chrM_3504_4052_0:0:0_0:2:0_b9
+CCAGAACTCTACTCAACTAACTTCATAATAGAAGCTCTACTACTATCATCAACATTCCTATGGATCCGAG
+>chrM_3542_4113_1:0:0_0:0:0_65
+ACTACTATCATCAACATTCCTATGGATCCGAGCATCTTATCGACGCTTCCGTTACGATCAACTTATACAT
+>chrM_3560_4153_2:0:0_1:0:0_4f
+CCTATGGATCCGAGCATCTTATGCACGCTTCCGTTACGATCAACTTATACATCTTCTATGAAAAAACATT
+>chrM_3562_4117_0:0:0_3:0:0_51
+TATGGATCCGAGCATCTTATCCACGCTTCCGTTACGATCAACTTATACATCTTCTATGAAAAAACTTTCT
+>chrM_3135_3669_1:2:0_1:0:0_2c
+AAGAAATATGTCACATACATAATGCTAGAGTTAGGGGTAGAAAGTTTTTTCATAGAAGATGTATAAGTTG
+>chrM_3422_3872_1:0:0_2:1:0_3b
+CCCTATAGCTTAATTAGCTGACCTTAGTATTAGGATAAGGTGTTTAGGTAGCAAGGAGAATTTTGAATTC
+>chrM_3587_4003_0:0:0_1:1:0_a7
+TCATATCAGTATTAGGTTGGTGCTGGATATTGTGATTACAGGACCTAATAAGATTGTGAAGTAGATGATG
+>chrM_3998_4489_2:1:0_1:1:0_be
+ATATGAGAAGGCCTGGAATTCCGCCAACTAGCAATTATCCCCATACTAATCAACAAAAAAAACCCACGAT
+>chrM_4007_4449_2:0:0_3:1:0_17
+GTCCTGGAATTCAGCCTACTAGCACTTATCCCCATACTAATCAACAAAAAAAACCCACGATCAACTGAAG
+>chrM_4139_4621_1:0:0_4:0:0_7e
+CTCAACTATAAACAACTAGGAACATGAATATTTCAACAACAAACAAACTGTCTTATCCTTAACATAACAT
+>chrM_4200_4733_4:0:0_0:1:0_6f
+ACATCAGATTAATAGCCCTAACCATAAAACTAGGCCTCGCCCCATTCCACTACTGATTACCAGAAGTAAC
+>chrM_3799_4278_3:2:0_1:0:0_1d
+TTAAGAATTCAAAATTCTGCTAGCTACCAAAACACCTTATCCTGATAGTAAGGTCAGCTAATTAAGCTAT
+>chrM_4256_4777_1:0:0_2:2:0_66
+TTACCAGAAGTAACTCAAGGGATCCCACTGCACATAGGACTTATTCTTGTTACATGACAAAAAATTGCTC
+>chrM_3889_4361_3:0:0_3:0:0_33
+TGAGTAGCGGGTAAATTTGACTTAAAATTGAAAGGGGCGCAATTTTTTGTCATGTAAGAAGAATAAGTCC
+>chrM_3912_4414_3:0:0_2:1:0_91
+TCATGCCCCAATGAAAATAGAAGTAAATGCTAGTATTAAAATGATAGTAGAGTTGAGTATCGGGTAAATT
+>chrM_3945_4422_1:2:0_0:1:0_64
+AGTCCTCCTCATGCCCCAATGAAAATAGAAGTAATTGCTAGTATTAAAATGATAGTAGAGTTGAGTAGCG
+>chrM_4354_4860_0:1:0_1:0:1_b1
+GCTACTCAACTCTACTATCATTTTAATACTAGCAATTACTTCTATTTTCATAGGGGCATGAGGAGGATTT
+>chrM_4383_4859_1:1:0_0:0:1_90
+TAGCAATTACTTCTATTTTCATAGGGGCATTAGGAGGATTTAACCAAACACAAATACGAAAAATTATAGC
+>chrM_4425_4987_2:0:0_2:3:0_35
+GCTTTGATTGCTCGCGGACTGGTAAATCCTAACCTTCTAGGTAATTAGTTGGGGGGCTAGGGGTAGGGTT
+>chrM_4427_4991_1:0:0_3:3:0_7
+CAAACACAAATACGAAAAATTATAGCCTATTCATCAATTGCCCACCTAGGATGAATATTAGCAATTCTTC
+>chrM_4480_4986_1:1:0_2:3:0_98
+AAAATTAGCAATTCTTCCTTACAACCCATCCCTCACTCTACTCAACCTCATAATGTATATTATTCTTACA
+>chrM_4491_4937_1:0:0_1:1:0_5e
+TTCTTCCTTACAACCCATCCCTCACTCAACTCAACCTCATAATCTATATTATTCTTACAGCCCCTATATT
+>chrM_4079_4594_1:0:0_3:0:0_28
+GATGGTTATAGCGTTATTTAGTATAAGTGCTATGAATCTAGGGGCTGTAAGAATCATATAGATTATGAGG
+>chrM_4140_4598_2:0:0_2:0:0_12
+AGATGATGGTTATAGAGTTATTTAGTATAAGTGCTATGAATAAAGGGGCTGTAAGAATAATATAGATTAT
+>chrM_4627_5166_2:0:0_2:1:0_13
+AGCAATACTACCTATAATCTCAGTGATATTACTATCCCTAGGAGGCCTTCCACCACTAACAGGATTCTTA
+>chrM_4810_5337_0:1:0_0:3:0_9c
+CACTTCACTAACAATATTTCCAACCAACAATAACTCAAAAATAATAACTCACCAAACAAAAACTAAACCT
+>chrM_4306_4893_3:0:0_3:1:0_83
+GAAAATATTAGGTTATGTTTAGTTTTTGTTTGGTGAGTTATTAATTTTGAGTTATTGTTGGTTGGCAATA
+>chrM_4842_5304_1:1:0_0:2:0_41
+CCTCAAAAATAATAACTCACCAAACAAAAACTAAACCTAACCTAATATTTTCCACCCTAGCTATCATAAG
+>chrM_4484_4978_1:2:0_1:2:0_3d
+GCTCGCGGACTGGTATATCCTAACCTTCTAGGTAATTAGTTGGGGGGCTCGGGGTAGGGTTATTGTGCTT
+>chrM_4918_5435_0:2:0_1:1:0_74
+TAAAATACTTAGTGCAGTACCCACTATTCCCGCTCAGGCTCCGAATAGTAGAAAGAGGGTTCGGATATCT
+>chrM_5540_5928_2:2:0_1:0:0_2d
+ACCAATAATAATTGGTGGCTTTGGCAACTGACTTGTCCCACTAATAATCGTAGCCCCAGATATAGCATTC
+>chrM_5583_6032_2:0:0_3:1:0_2b
+ATACTCGGAGCCCCAGATATAGCATTCCCACGAATAAATAATATAAGTTTTTGAGTCCTACCACCATCAT
+>chrM_5645_6067_1:2:0_1:3:0_1c
+ACCATCATTTCTCCTTCTCCTAGCATCATCAATAGTAGAGGCAGGAGTAGGAACATGATGAACAGTCTAC
+>chrM_5770_6257_3:0:0_1:2:0_46
+TCTCCCTTCATTTAGCAGGAGTGTCATCTATTTTAGGTGCAATTACTTTTATTACCACTATTCTCAACAT
+>chrM_5340_5854_0:1:0_0:0:0_a
+ATGGCTGGGGGTTTCATGTTGATAATAGTGGTAATAAAATTAATTGCACCTAAAATAGATGACACTCCAG
+>chrM_5499_5905_2:3:0_1:0:0_2f
+ACGGGTGTAATAAGTACGGATCAGACAAATAGTGGAGTTTGATACTGTGTTATGGCTGGGGGTTTCATGT
+>chrM_5451_5933_2:1:0_1:1:0_57
+TAACACTTGTAGTGATAATAGGAGCAGTACGGCTGTAATAAGTACGGATCAGACAAATAGTGGAGTTTGA
+>chrM_5403_5984_0:0:0_1:2:0_ab
+GAAAGTTTTGTTTAGGTTGCGGTGTGTTAGTAGTATAGTAATGCCTGCGGCTAACACTGGTAGTGATAAT
+>chrM_5930_6421_2:3:0_1:1:0_2e
+GTTAGCCGCAGGCATTACTATACTACTACCAGACCGCAACCTAAACACAACTTTCTTTGATCCCGCGGGA
+>chrM_5615_6110_2:1:0_0:3:0_14
+GTAGTAAGTAACTACATGTGAAATAATTCCAAATCCTGGGAGGATAAGAAAAAAAACTTCTGGGTGCCCC
+>chrM_6074_6685_2:0:0_0:2:0_a3
+AGGATTTGGAATTATTTCACATGTAGTTACTTACTACTCCGGCAACAAAGAACCTTTCGGCTATATAGGA
+>chrM_5831_6292_0:0:0_1:0:0_15
+CTAAATACTTTGACACCGGTAGGACTTGCGATAATTATAGTGGCTGATGTAAAGTAAGCTCGTGTGTCTA
+>chrM_6228_6791_1:0:0_0:0:0_ae
+ACACGAGCTTACTTTACATCAGCCACTATAATTATCGCAATTCCTACCGGTGTCAAAGTATTAAGCTGAC
+>chrM_6246_6734_0:0:0_1:0:0_69
+TCAGCCACTATAATTATCGCAATTCCTACCGGTGTCAAAGTATTTAGCTGACTTGCAACCCTACACGGAG
+>chrM_6261_6802_2:0:0_2:0:0_87
+ATGGCAATTCCTACCGGAGTCAAAGTATTTAGCTGACTTGCAACCCTACACGGAGGTAATATTAAATGAT
+>chrM_5910_6386_0:2:0_1:1:0_1e
+TAGACCACCAACTGTAAATAAGAAAATAAAGCCTAAGGCTCATAGTATAGCTGGAGATCAGTTAAAATTA
+>chrM_6356_6909_2:1:0_4:0:0_72
+CTTTATTTTCTTATTTACCGTTGGTGGTCTAACCGTAATTGCTTTATCCAACTCATCCCTTGACATCGTG
+>chrM_6366_6887_1:1:0_3:0:0_85
+TTATTTACAGTTGGTGGTCTAACCGTAATTGCTTTATCCAACTCATCCCTTGACATCGTGCTTCACGATA
+>chrM_5959_6526_0:2:0_1:2:0_c5
+AATAATGTGAATCAGTGAACAAATCCTGCTATGATAGCAAACACTCCTCCCATTGATGGAACATAGTGGA
+>chrM_6458_6985_2:2:0_1:0:0_b5
+CCACTATGTTCCATCAATGGGAGGAGTGTTTGCAATCATAGCAGGATTTGTTCACAGATTCCCATTATTT
+>chrM_6510_7029_2:1:0_1:0:0_16
+CACTGATTCCCATTATTTTCCGGGTTCACCCTAGATGACACATGAGCAAAAGCCCACTTCGCCTTCATAT
+>chrM_6138_6598_0:0:0_1:2:0_6e
+GTTATGTTCACTCCTACGAATATGAAGTCGAAGTGGGCTTTTGCTCATGTGTCATCTAGGGTGAAGCCTG
+>chrM_6719_7233_1:0:0_4:1:0_b0
+TGTTCTCATCATGATCTTTATAATTTGAGAGGCCTTTGCTTCAAAACGATAAGTAATATCAGTATCGTAT
+>chrM_6720_7201_2:1:0_1:0:0_b8
+TTTCTCATCATGATCTTTATAATTAGAGAGGCCTTTGCTTCAAAACGATAAGTAATATCAGTATCGTATG
+>chrM_6367_6804_0:1:0_1:1:0_5d
+CTAAATTTGTTGAATCATACGATACTGATATTACTTATCGTTTTGAAGCAAAGGCCTCTCAAATTATAAA
+>chrM_6845_7289_0:0:0_4:0:0_5c
+GGAACCAACCTATGTAAAAGTAAAATAAGAAAGGAAGGAATCGAACCCCCTAAAATTGGTTTCAAGCCAA
+>chrM_6864_7309_1:0:0_0:0:0_a6
+GTAAAATAAGAAAGGAAGGAATCGAACCCCCTAAAATTGGTTTCAAGCCAATCTCATATCCTATCTGTCT
+>chrM_6514_6987_2:1:0_1:0:0_8
+TAATTTAACTTTGACAAAGTTATGTAATTGATTTTACTAATATCTTATTGAGAAAGACATATCGGATATG
+>chrM_7046_7557_1:0:0_2:2:1_c6
+GCCACATCCCCTATTATAGAAGAGCTAATAAATTTCCATGATCACACACTAATAATTGTATTCCTAATTA
+>chrM_7156_7672_2:1:0_0:0:0_53
+AAACCTAACACATACAAGCACAATAGATGCACTAGAAGTTGAAACCATTTGAACTATTGTACCAGCTGTA
+>chrM_7258_7724_0:1:0_0:0:0_10
+CATTCTATATATAATAGACGAAATCAACAACCCCTTATTAACCGTTAAAACCATAGGGCACCAATGATAC
+>chrM_7339_7816_1:0:0_3:4:0_43
+AATTGATGAGATAATTGTGATAATTCATGTTGAAGTATCTAGTTGTGGGTTAGCACAATGGAGATTTTAA
+>chrM_6938_7424_2:0:0_1:0:0_b4
+CTTCTAGCAGTCGTAGTTCACCAGGTTTTCGGTCGTTTGTTGGGATTATATATGAATCAAAGCATAGGTC
+>chrM_7188_7644_1:1:0_2:1:0_a9
+AGGACAATGGGCATAAAGCTATGGTTCGATCCACAAATTTCAGAGCATTGGCCATAGAATAACCCTGGTC
+>chrM_7668_8147_1:1:1_1:2:1_6b
+TCGAAAACTGATCTGCTTCAATCATTTAATTTCACTATGAAGCTAAGAAGCGTTAACCTTTTAAGTTAAA
+>chrM_7223_7762_2:1:0_1:1:0_a1
+ACAATGGAGATATTAAGGTCTCTAACTTTAACTTAAAAGGTTAACGCTCTTAGCTTCATAGTGAAATTAA
+>chrM_7358_7894_0:0:0_1:0:1_bc
+TTTTAGGATTTTGGTGAAGGTGCCAGTGGGAATGTTTGTGATGAGACTTTTAGTTGAAATAAGATAAATA
+>chrM_7550_8033_2:2:0_0:0:0_26
+AATCAAGCAACAGCAACATCCAACGGACCCGGGTTATTCTATGGCCAATGCTCTGAAATTTGTGGATCTA
+>chrM_7964_8497_0:0:0_2:0:0_8c
+CAATAATAGGATTCCCAATCGTTGTAGCCATCATTATATTTCCTTCAATCCTATTCCCATCCTCAAAACG
+>chrM_7785_8278_5:1:0_2:0:0_99
+GGAAGCCTGTAATTACGGCTGCAGCTCATAGTGGAATGGCTATACTTAGATTTATGGATATTTGGGTAGT
+>chrM_7728_8283_1:4:0_2:0:0_1b
+GTGTCGGAAGCCTGTAATTACGGCTCCATCTCCTAGTGGAATGGCTATACTTAGATTTATGGATAGTTGG
+>chrM_7788_8291_0:0:0_3:1:0_86
+TTAAGTTTGTGTCGGAAGCCTGTAATTAGGGCTCCAGCTCATAGGGGAATGTCTATACTTAGATTTATGG
+>chrM_7835_8385_1:0:1_2:0:0_c7
+TGGTAGAATAAATAGGCTAATTGTTTCAATAATAATAATTATTGGAATTAGTGAAATTGGAGTTCCTTGT
+>chrM_8325_8781_1:0:0_2:0:0_9d
+TCCAATTTCACTAATTCCAATACTTATTATAATTGAAACAATTAGCCTATTTATTCAACCAATGGCATTA
+>chrM_7872_8415_2:0:1_1:0:0_1a
+GTTAGCTGTAAGCCGGACTGCTAATGCCATTGGTTGAATAAATAGGCTAATTGTTTCAATCATAATAAGT
+>chrM_7939_8482_1:1:0_2:0:0_25
+GGCTAATATTTATTAATACTAGAGTAGCTCCTCCGATTATGTGTATTAATAAGTGTCCTGCAGAAATGTT
+>chrM_8733_9211_0:0:0_0:0:0_47
+TTAACCCTTGGCCTACTCACCAATATCCTCACAATATATCAATGATGACGAGACGTAATTCGTGAAGGAA
+>chrM_8419_8906_1:0:0_3:0:0_9f
+CGGTGAGAAGAATGCTGCAAAGAAAAATACTTCCGAGACGATGAATAGAATTATACCATATCGTAGTCCT
+>chrM_8886_9293_2:1:0_0:0:1_a2
+TTTGGAGGATTCTTCTGAGCGTACTATCATTATAGCCTCGTACCAACACATGATCTAGGAGGCTGCTGAC
+>chrM_9032_9593_1:2:1_1:0:0_b2
+TTCATTACATGACCTCATTATAGCCTTATAGAAGGTAAACGAAACCACATAAAACAAGCCCTACTAATTA
+>chrM_8761_9187_1:1:0_0:0:0_ba
+CCATAGATACCATCTGAAATGGAGAATGATGTTTCAAAGTATTCTGAAGCTTGGAGGATGGTGAAGTAAA
+>chrM_9120_9714_1:1:0_0:1:0_88
+TACTTCACCATCCTCCAAGCTTCAGAATACATTGAAACACCATTCTCCATTTCAGATGGTATCTATGGTT
+>chrM_9142_9548_1:1:0_1:2:0_77
+CAGAATACTTTGAAACACCATTCTCGATTTCAGATGGTATCTATGGTTCTACATTCTTCATGGCTACTGG
+>chrM_9150_9818_1:1:0_1:1:0_bf
+TTTGAAACACCATTCTCCATTTCAGATGGTATCTAAGGTTCTACATTCTTCATGGCTACTGGATTCCATG
+>chrM_8863_9244_0:0:0_1:0:0_92
+GTTGATCCAATAATTACATGGAGTCCATGGAATCCAGTAGCCATGAAGAATGTAGCACCATAGATACCAT
+>chrM_8794_9257_1:1:0_1:0:0_79
+AAGAATAAGGAATGTTGATCCAATAATTACATGGAGTCCATGGAATCCAGTAGCCATGAAGAATGTAGAA
+>chrM_9222_9781_2:0:1_1:0:0_23
+CTCCATGTAATTATTGGATCAACATTCCTTCTAGTTTGCCTACTAGACAACTAAAATTTCACTTCACATC
+>chrM_9038_9471_1:3:0_1:1:0_8a
+TGTACAGGTTAATTACTCTGTTCTGGGTTTATTCAGAATCTACTAATTGGAAGTCAGTTCTATTAATTAT
+>chrM_9031_9522_3:3:0_2:0:0_84
+ATGGAACTAGAATTAGCGTTAGGGATAATAAAATATTAATGAAGATAACAGTGTACATGTTAATTACTCT
+>chrM_9505_10155_3:0:0_1:0:0_9a
+CGCTACTTCTAGTTGCATTCTGACTCCCCCAAATACATCTGTCCTCAGAAAAAGCAAATCCATATGAATG
+>chrM_9647_10116_2:0:0_1:2:0_2a
+ATTATTTGACCTAGCAATTGCTCTTCTACTTCCACTACCATGAGCAATTCAAACAATTAAAACCTGTACT
+>chrM_9409_9920_3:1:0_1:0:0_d
+GATAGAGAGAAGGCTATGGTGAGGTTGAAGAAGGTAGATGGCATATTGGTAATTATGAACATCATCATAA
+>chrM_9897_10466_3:1:0_1:0:2_1
+CCTCACCATAGCCTTCTCACTATCACTACTAGGAACACTTATATTTCGCTCACACCTCATATCCACATTA
+>chrM_9907_10368_2:0:0_1:0:0_c2
+GCCTTCTCACTATCCCTTCTAGGGACACTTATATTTCGCTCTCACCTAATATCCAGATTACTATGCCTGG
+>chrM_9910_10411_1:1:0_0:1:2_bb
+TTCTCACTATCACTTCTAGGAACACTTATATTTCGCTCTCACCTAATATCCACATTACTATGCCAGGAAG
+>chrM_9496_9991_0:0:0_3:1:0_80
+CTAATACTATGCCTTCCAGGCATAGTAAAGTGGATATTAGGTGAGAGCGAAATCTAAGTGTTCCTAGAAG
+>chrM_10106_10577_3:1:0_2:0:0_5b
+AACTAGTAAAAGTTTCAAACACGAACGGAACAGATTACGTCCAAAATCTCAACCTGCTACAATGGTAAAA
+>chrM_10193_10658_0:2:0_1:0:0_b6
+AATGCTACTCCCACTAACCTGACTATCAAGCCCTAAAAAAACCTGCACAAACGTAACCTCATATAGTTTT
+>chrM_9735_10262_1:0:0_1:2:0_40
+AAAACTATATGAGGTTACGTTTGTGCAGGTATTTTTAGGGCTTGATAGTCAGGTTAGTGGGAGTAGCATT
+>chrM_10206_10702_1:0:0_3:1:0_9e
+CTAACCTTACTATCAAGCCCTAAAAAAACCTGAACAAACGTAACCTCATATAGTTTTCTAATTAGTTTAA
+>chrM_10254_10719_0:0:0_1:1:0_8e
+TATAGTTTTCTAATTAGTTTAACCAGCCTAACACTTCTATGACAAACCGACGAAAATTATAAAAACTTTT
+>chrM_10023_10620_2:2:0_3:0:0_4
+AAACTCCAACTCCATAAGCTCCATACCATTCCCCATCACGATCGTAGTTATCGCAGCCTGCGAAGCAGCT
+>chrM_10203_10663_1:0:0_1:0:0_42
+AAGATGAGGGCAATTAGCAGTGGAATAGAACCGATTCGGGTATAAAATAGGAAATAAATCCCTGCGTTTA
+>chrM_10362_10821_2:1:2_0:0:0_c
+CTTTTGGTAGTCATAGGTGAACTCCATATAATGGTATTTTAATAAGAAATGCTATTATGCATGCCAACCA
+>chrM_10389_10966_1:0:0_1:0:0_61
+CATAGGGAGAGAAGGAAGAAGGGGTATGCTATATATTTTGTTAGTGGGTCTAGAATAATGGAGATGCGAA
+>chrM_10461_11010_1:1:0_0:0:0_21
+AATCTGTTTGGCGTAAGCAGATTGAGCTAGTTATAATTATTCCTCATAGGGAGAGAAGGATGAAGGGGTA
+>chrM_11041_11475_1:0:0_1:1:0_7b
+GCCACATAGCACTTGTTCTTGCATCAATCATAATCCAAACTCCATGAAGCTTCATAGGAGCAACAATACT
+>chrM_10767_11161_1:0:0_2:0:1_39
+GAGTTTGCTAGGCAGAATAGGAGTGATGATGTGAGGCCATTTTCGATTATTAGTATTTTGCTCCTATGAA
+>chrM_11211_11625_0:1:0_2:0:0_37
+CAAATGGTCTTACCACTTATAGCCACATGATGACTGATAGCAAGTCTAGCTAATCTAGCTCTACCCCCTT
+>chrM_11475_12014_1:1:0_2:1:0_56
+ATAGCCCTTCACATAATTCCACTTATTATTCTAACTACCAGTCCAAAACTAATTACAGGCCTGAGAATAT
+>chrM_11195_11669_2:0:0_1:0:0_49
+AGCAAGCCATGTTTTTAAACATGGAAGCATGAATTAGCAGTTCTTGCAATCTTTCTTGGTGAATAAGGAG
+>chrM_11464_11999_0:1:0_3:1:0_3a
+AGAGAAAAAGTTCGTTTTTAAGCATATTTTAAGTTCTATTGAATTTATGGTGACTCAGTGCCAGGTTGTA
+>chrM_12174_12610_1:1:0_0:0:1_93
+GAAGGTGTGGGAATTATATCTTTCCTACTAATTGGATGATGGTACGGACGAACAGTCGCAAATACTGCAG
+>chrM_11715_12248_2:1:0_1:1:1_a0
+TAGGGCTGCAGTATATGCGACTGTTCTCCGTACCATCATCCAATTAGTAGGAAAGATATAATTCCCACCC
+>chrM_12218_12618_2:1:1_1:1:0_32
+CGGAGAACCGTCGCAAATACTGCAGCCCTACAAGCAATCCTCTATAACCGCATCTGAGACATCGGATTCA
+>chrM_12243_12713_2:0:0_1:0:0_bd
+GCCCTCCAAGCAATCCTCTATACCCGCATCGGAGACATCGGATTCATTTTAGCTATAGTTTGATTTTCCC
+>chrM_12113_12598_3:3:0_2:0:1_70
+CCTGTTTACCATGCTTATCCTCACCTCAGCCAACCACATATTTCAACCTTTCATTGGCTGAGCAGGGTTT
+>chrM_12064_12604_0:1:0_1:0:1_aa
+GTAAATAATGTGGTTAGGGCTCCGAGGCAAAGTATAGTTGTTAAAATAAAGTTAATATTAGCGTGAGGGG
+>chrM_12577_13079_0:0:0_1:1:1_11
+ATTTTGGTTAATGGAGATGTAGGGGGGGAAAAGGCGGTTTTGTTATTGTTACGAAGTAAATGATTCGTAT
+>chrM_12622_13091_0:0:0_3:0:1_78
+CCCAAAACGACATCAAAAAAATCATTGCCTTCTCTACATCAAGCCAACTAGGCCTGATAATAGTGACGCT
+>chrM_12705_13147_4:0:0_2:0:0_94
+CGACACCTAGCATTCCTACACATCTGTACCCACGCAATGTTCAAAGCTATACTCTTTCTATGCTCTGGCT
+>chrM_12275_12781_1:0:0_1:0:1_6
+ATGATTGAGCGAGAGCATATAGAAGAGTATAGCTTTGAAGAATGCGTGGGTACAGATGTGTAGGAATGCT
+>chrM_12355_12806_0:1:0_1:0:0_6a
+GTCTTGTTCGTCTGCCAGGCTATGAATTATTGAGCCAGAGCATATAAAGAGTATAGCTTTGAAGAATGCG
+>chrM_12440_12937_5:0:0_1:0:0_8b
+ATTGCTTCAATAATTAGGTCTTTTGAGTAGAACCCTGTTAGGAATGGTATTCGTGTGAGGGCGAGGCTTC
+>chrM_12640_13011_2:0:0_2:1:0_62
+TGCTGTACATAGCTGTCATCGAAGTGGGGATTAGTGTAATTAGTAGGGCTCAGGCGTTGGTGTTGCAGGT
+>chrM_12982_13475_3:1:0_2:0:1_75
+TCGCCACTTCTATGACAGCTATGAACAGCATACGACTCATTTACTTCGTAACAATCACAAAACCGCGTTT
+>chrM_12720_13279_1:0:1_2:0:0_2
+ATTGCTAGTTTTATGGTTAGGTTGTTTAGTTCTAGTGCGATTAGTAATCCTAATACTGAAATAATTAGGG
+>chrM_12881_13337_0:0:0_1:1:0_89
+AATAGATGGTAAAAACCCCAGTAAACTTGAGAAGGATGAATATGGATTTGCTTTATTTATTGATAGTTTT
+>chrM_13281_13783_1:1:0_1:0:0_67
+AATAAAGCAAATCCATATTCATCCTTCACAAGTTTACTGGGGTTTTTCCCATCTATTATTCACCGCATTA
+>chrM_13494_14044_3:1:0_1:1:0_7d
+AAATTGTACATTATATCATTCCTAATTAACATCATCTTAATTATTATCTTTTACTCCAATAATCTCGAGT
+>chrM_13142_13600_1:0:0_1:2:0_34
+ATCTTTGTTTGCGGGTATTTTTGTTATTATAGAGATTACTCGAGATTAATTGAGTATAAGAAAATAATTA
+>chrM_13326_13750_2:0:1_2:1:0_82
+TTATTATGATGAAGTTGGAGTAATTACTCTTGATGGTATGGGAGATTGGTTGATGTATTAGGTTGATGAT
+>chrM_13198_13763_2:0:0_0:1:0_7c
+TTTGTGTGCTTAATTATTATGATGAAGTTGGAGTAATTAATCTTGATGGTATGGGAGATTGGTTGATGTA
+>chrM_13715_14154_1:0:0_1:1:0_96
+CCATCACGATTAATTACTCCAACTTCATCATAATAATTAAGCACACAAATTAAAAAAACCTCTATAATCA
+>chrM_13338_13860_2:1:1_2:0:1_4d
+ATTCACCGCATTACACCCATAAAATTCTGAACCTAAGCCTAAAAACATCCCTGACTCTCCTAGAGTTGAT
+>chrM_13813_14351_0:1:0_0:1:0_1f
+TCAGTTAGATCCCCAAGTCTCTGGATATTCCTCAGTAGCTATAGCAGTTGTATATCCAAACACAACCAAC
+>chrM_13482_13976_0:0:0_1:2:0_c1
+TAATTGTTACTGGGTTTGTTGGTCGTTTAATGGTTTTAGGGTTTGGTTGATCGTTTTTAGGTTTAATAGT
+>chrM_13910_14543_2:1:0_1:1:0_30
+ATTAAACCTAAAAACGATCCACCAAACCCTAAAACCATTAAACGAGCAACAAACCGACTAACAATTAAAC
+>chrM_13936_14395_2:2:0_1:1:1_76
+CCCTAAAACCATTAAACGACCAACAAACCCAGTAACCATTAAACCTAAACCTCCATAAATAGGTGAATGC
+>chrM_13940_14475_1:1:0_3:2:0_27
+AAAACCATTAAACGACCAACAAACCCACTAACAATTAACCCTAAACCTCCATAAATAGGTGAAGGCTTTA
+>chrM_14052_14489_0:0:0_3:4:0_4c
+CAAAAATATAATTATTCATTATTTCTACACAGCATTCAACTGCGACCAATGACATGAAAAATCATCGTTG
+>chrM_14105_14613_0:0:0_2:0:0_48
+ATGAAAAATCATCGTTGTAATTCAACTACAGAAACACCTAATGACAAACATACGAAAAACACACCCATTA
+>chrM_14128_14614_0:1:0_1:1:0_97
+AACTACAGAAACACCGAATGACAAACATACGAAAAACACACCCATTATTTAAAATTATTAACCACTCATT
+>chrM_14131_14628_2:1:0_2:1:0_36
+TACAGAAACACCGAATGACAAACATACGACAAACACACCCATTATTTAAAATTATAAACCACTCATTCAT
+>chrM_13791_14330_0:0:0_3:0:0_29
+GGCTGTTATTGTAACTGATGTGTAGTGAATGGCTAAGAAAAGACCTGTAATGATTTGGACTATAAGGCAG
+>chrM_13944_14351_1:1:0_0:0:0_44
+AATGTGTGTTACTGATGAAAAGGCTGTTATTGTATCTGATGTGTAGTGTATGGCTAAGAAAAGACCTGTA
+>chrM_13992_14451_1:1:0_1:3:0_52
+ATAAGCCTCGTCGGAGCTGAAGGAACAAGCAAATAAAAAATATTGAGGCTCCGTTTGCGTGTATATATCG
+>chrM_14442_15026_1:2:0_3:0:0_60
+CGAGGCTTATATTATGGATCAGATACATTTATAGAAACCTGAAACATTGGAGTACTTCTTCAGTTCGCAG
+>chrM_14576_14894_2:0:0_0:0:0_5f
+AGTTATTCCAAACCTCCTATGAGCCATCCCATATATTGGAACAACCCTAGTCGAATGAATTTGAGGGGGC
+>chrM_14707_15163_1:1:0_1:2:0_9
+TTATCGGGGCCCTAGCAATCGTTCACCTCATCTTCCTCCACGAAACAGGATCAAACAACCCAACAGGATT
+>chrM_14728_15189_1:2:0_2:0:0_7a
+TTCACCTCATCTTCCTCCACGAAACAGGATCAAACCACCCAACAGGATTATACTCAGATGCAGATAAAAT
+>chrM_14794_15314_1:0:0_1:0:0_c0
+AAATTCCATTTCACCCCTACTATACAATCAAAGATATCCTAGGTATCCTAATCATATTCTTAATTCTGAT
+>chrM_14975_15480_1:0:1_0:1:0_4e
+ATACGCCATTCTACGCTCCACTCCCCAATAAACTAGGAGGTGTCCTAGCCTTAATCTTATCTATCCTAAT
+>chrM_15196_15749_1:1:1_2:1:0_c4
+GCTAACTAGCCCCATCTCATACTTCTCAATCATCTTAATTCTTATACCAATGTCAGGAATTATCGAAGAC
+>chrM_14768_15298_0:1:0_1:1:0_ac
+CTATCAAGACATGGATATAATTTTAGTATTTTGTCTTCGATAAGTCCTGAGCTTGGTATAAGAATTAAGA
+>chrM_14885_15311_3:1:0_1:0:0_3
+AGTAATGTTTATACTATCAAGACATGGATATAATTTTAGTATTTTGTCTTCGATAATTCCAGAGATTGGT
+>chrM_14820_15346_1:0:0_0:0:0_5a
+AAGAGAAGATCTTCATTTCAGGTTTACAAGACCAGAGTAATGTTTATACTATCAAGACATGGATATAATT
+>chrM_14858_15398_0:0:0_3:0:0_b3
+CAGCTTTGGGTGCTGGAGGTGGGTAGTAGCTCCTTCTTCTTGATGTCTTGAGAAGAGCAGATCTTCATTT
+>chrM_15417_15889_0:0:0_2:0:0_50
+TTCTTGAGTACATAAATTTACATAGTACAACAGTACATTTATGTATATCGTACATTAAACTATTTTCCCC
+>chrM_14988_15504_0:0:0_1:1:0_38
+GTATTAGCTTATATGCTTGGGGAAAATAGTTTAATGTACGATATACCTAAATGTACTGTTGTACTATGTA
+>chrM_15462_15945_2:1:0_0:0:0_0
+TATCGTACATTAAACAATTTTCCCCAAGCATATAAGGTAATACATTAAATCAATGGTTCAGGTCATAAAA
+>chrM_15171_15615_1:0:0_0:1:0_c3
+TAACACAGATATGTCCTTATAACATTAGTTTAATGTGTTTAAGATAATATTCATGGTATATATATTGGTT
+>chrM_15361_15805_1:0:0_2:0:0_81
+TGAAGTAAGAACCAGATGTCTTATAAAGTTTCAGTTTAGCTACCCGCAAGTTTAATGGGCCCGGAGCGAG
+>chrM_15481_15968_1:2:0_2:0:0_6d
+GTCCTTACATGCCTTGACGGCTATGTTGATGAAAGTAGGCCAAAATAAAAAGATCCCAAATGCATGACAC
+>chrM_15523_16020_2:1:0_1:1:0_31
+GGGTTTTGCGGACTAATGATTCTTCACCTAAGGTGCGTCTAGACTGTGTGCTGTCCTTTCATGCCTTGAC
+>chrM_15549_16044_0:1:0_1:1:0_59
+ATGAATAATTAGCCTTAGGTGATTGGGTTTTGCGGACTAATTATTCTTCACCGAAGGTGCGTCTAGACTG
+>chrM_15720_16131_0:1:0_2:1:0_58
+TGTTTATGGGGTTTGGCATTAAGAGGACGGGGTGGGGGGTTTTGAGAGTTAAAATTTGGTATTGAGTAGC
+>chrM_15642_16224_2:1:0_0:0:0_a5
+AGTACTAAAATATAAGTCATATTTTGGGAACTACTAGAATTGATCAGGACATAGGGTTTGATAGTTAATA
+>chrM_15820_16268_3:1:0_1:0:2_7f
+TTAGAGTTTTGGTTCACGGAACATGATTTTGTAAAATTTTTACAAGTACTAAAATAAGTCATATTTTGGG
+>chrM_13991_14484_3:1:0_3:4:0_20
+TAAATAGGTGAAGGCTTTAATGCTAACCCCAGACAACCAACCCAAAATAATGATCTTAAAACCAAAATAT
+>chrM_8781_9305_4:1:0_3:0:1_3e
+TAAGTGATGTTTTGATGTGCAGTGAAATTTTAGTTTTCTAGTAGGCAAACAATAAGGAATGTTGATCCAA
+>chrM_14312_14826_2:1:1_4:1:0_a4
+CTTTGATTTTATAGTAGGGGTGAAATGGACATTTATCTGCATCTGAGAATAATCCTGTTGGGTTGTTTGA
+>chrM_408_812_0:2:1_4:2:0_ad
+TGAAAAATCATTGTTAGGACCTAAACCGTCAATAACGAAAGTAATTCTACTCATTTATAATACACGACAG