# HG changeset patch
# User iuc
# Date 1619123113 0
# Node ID 1ca4ce7241fd52810e47a05758099f49ac7b20ad
# Parent  a7228a7ea1468b751e21ec134458440447d2e6c6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"

diff -r a7228a7ea146 -r 1ca4ce7241fd annotateVCF.py
--- a/annotateVCF.py	Mon Mar 29 20:06:44 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,409 +0,0 @@
-#!/usr/bin/env python3
-
-# Takes in VCF file and a samtools mpileup output file
-# Fills in annotation for the VCF file including AF, DP
-# SB, and DP4
-#
-# Usage statement:
-# python annotateVCF.py in_vcf.vcf in_mpileup.txt out_vcf.vcf
-#
-# Can generate in_mileup.txt with samtools mpileup (and can restrict which sites to generate pileups for with in_vcf.vcf)
-
-# 08/24/2020 - Nathan P. Roach, natproach@gmail.com
-
-import sys
-from math import isnan, log10
-
-from scipy.stats import fisher_exact
-
-
-def pval_to_phredqual(pval):
-    return int(round(-10. * log10(pval)))
-
-
-def parseSimpleSNPpileup(fields, ref_base, alt_base):
-    base_to_idx = {
-        'A': 0,
-        'a': 0,
-        'T': 1,
-        't': 1,
-        'C': 2,
-        'c': 2,
-        'G': 3,
-        'g': 3
-    }
-
-    base_to_idx_stranded = {
-        'A': 0,
-        'T': 1,
-        'C': 2,
-        'G': 3,
-        'a': 4,
-        't': 5,
-        'c': 6,
-        'g': 7
-    }
-    ref_base2 = fields[2]
-    counts = [0, 0, 0, 0]
-    stranded_counts = [0, 0, 0, 0, 0, 0, 0, 0]
-    ref_idx = base_to_idx[fields[2]]
-    dp = int(fields[3])
-    carrot_flag = False
-    ins_flag = False
-    ins_str = ""
-    ins_len = 0
-    insertion = ""
-    del_flag = False
-    del_str = ""
-    del_len = 0
-    deletion = ""
-    # dollar_flag = False
-    for base in fields[4]:
-        if carrot_flag:
-            carrot_flag = False
-            continue
-        if ins_len > 0:
-            insertion += base
-            ins_len -= 1
-            continue
-        if del_len > 0:
-            deletion += base
-            del_len -= 1
-            continue
-        if ins_flag:
-            if base.isdigit():
-                ins_str += base
-            else:
-                ins_len = int(ins_str) - 1
-                ins_str = ""
-                insertion = base
-                ins_flag = False
-        elif del_flag:
-            if base.isdigit():
-                del_str += base
-            else:
-                del_len = int(del_str) - 1
-                del_str = ""
-                deletion = base
-                del_flag = False
-        else:
-            if base == '^':
-                carrot_flag = True
-                continue
-            elif base == '$':
-                continue
-            elif base == '+':
-                ins_flag = True
-            elif base == '-':
-                del_flag = True
-            elif base == '.':
-                counts[ref_idx] += 1
-                stranded_counts[base_to_idx_stranded[ref_base2]] += 1
-            elif base == ',':
-                counts[ref_idx] += 1
-                stranded_counts[base_to_idx_stranded[ref_base2.lower()]] += 1
-            elif base == 'N' or base == 'n':
-                continue
-            elif base == '*':
-                continue
-            else:
-                counts[base_to_idx[base]] += 1
-                stranded_counts[base_to_idx_stranded[base]] += 1
-    if sum(counts) == 0:
-        af = float("nan")
-    else:
-        af = float(counts[base_to_idx[alt_base]]) / float(sum(counts))
-    if float(sum(stranded_counts[0:4])) == 0:
-        faf = float("nan")
-    else:
-        faf = float(stranded_counts[base_to_idx_stranded[alt_base]]) / float(sum(stranded_counts[0:4]))
-    if float(sum(stranded_counts[4:])) == 0:
-        raf = float("nan")
-    else:
-        raf = float(stranded_counts[base_to_idx_stranded[alt_base.lower()]]) / float(sum(stranded_counts[4:]))
-    dp4 = [stranded_counts[base_to_idx_stranded[ref_base]],
-           stranded_counts[base_to_idx_stranded[ref_base.lower()]],
-           stranded_counts[base_to_idx_stranded[alt_base]],
-           stranded_counts[base_to_idx_stranded[alt_base.lower()]]]
-    return (dp, af, faf, raf, dp4)
-
-
-def parseIndelPileup(fields, ref_base, alt_base):
-    counts = [0, 0, 0, 0, 0, 0, 0, 0, 0]  # indel ref match, indel fwd ref match, indel rev ref match, indel alt match, indel fwd alt match, indel rev alt match, other, other fwd, other rev
-    ref_base2 = fields[2]
-
-    carrot_flag = False
-    ins_flag = False
-    ins_str = ""
-    ins_len = 0
-    del_flag = False
-    del_str = ""
-    del_len = 0
-    first_iter = True
-    forward_flag = False
-    last_seq = ""
-    last_seq_code = 'b'
-    for base in fields[4]:
-        if ins_flag:
-            if base.isdigit():
-                ins_str += base
-            else:
-                ins_len = int(ins_str)
-                ins_flag = False
-        if del_flag:
-            if base.isdigit():
-                del_str += base
-            else:
-                del_len = int(del_str)
-                del_flag = False
-        if ins_len > 0:
-            last_seq += base
-            last_seq_code = 'i'
-            ins_len -= 1
-            continue
-        if del_len > 0:
-            last_seq += base
-            last_seq_code = 'd'
-            del_len -= 1
-            continue
-        if carrot_flag:
-            carrot_flag = False
-            continue
-        if base == '.' or base == ','\
-                or base == 'A' or base == 'a'\
-                or base == 'C' or base == 'c'\
-                or base == 'G' or base == 'g'\
-                or base == 'T' or base == 't'\
-                or base == 'N' or base == 'n'\
-                or base == '>' or base == '<'\
-                or base == '*' or base == '#':
-            if first_iter:
-                first_iter = False
-            else:
-                if last_seq_code == 'i':
-                    if last_seq.upper() == alt_base.upper():
-                        counts[3] += 1
-                        if forward_flag:
-                            counts[4] += 1
-                        else:
-                            counts[5] += 1
-                    else:
-                        counts[6] += 1
-                        if forward_flag:
-                            counts[7] += 1
-                        else:
-                            counts[8] += 1
-                elif last_seq_code == 'd':
-                    if last_seq.upper() == ref_base.upper():
-                        counts[3] += 1
-                        if forward_flag:
-                            counts[4] += 1
-                        else:
-                            counts[5] += 1
-                    else:
-                        counts[6] += 1
-                        if forward_flag:
-                            counts[7] += 1
-                        else:
-                            counts[8] += 1
-                elif last_seq_code == 'b':
-                    if last_seq.upper() == ref_base.upper():
-                        counts[0] += 1
-                        if forward_flag:
-                            counts[1] += 1
-                        else:
-                            counts[2] += 1
-                    elif last_seq.upper() == alt_base.upper():
-                        counts[3] += 1
-                        if forward_flag:
-                            counts[4] += 1
-                        else:
-                            counts[5] += 1
-                    else:
-                        counts[6] += 1
-                        if forward_flag:
-                            counts[7] += 1
-                        else:
-                            counts[8] += 1
-            if base == '.':
-                last_seq = ref_base2
-                forward_flag = True
-                last_seq_code = 'b'
-            elif base == ',':
-                last_seq = ref_base2
-                forward_flag = False
-                last_seq_code = 'b'
-            elif base == '>' or base == '<' or base == '*' or base == '#':
-                continue
-            else:
-                forward_flag = base.isupper()
-                last_seq = base.upper()
-                last_seq_code = 'b'
-        elif base == '+':
-            ins_flag = True
-            ins_str = ""
-        elif base == '-':
-            del_flag = True
-            del_str = ""
-        elif base == '^':
-            carrot_flag = True
-        elif base == '$':
-            continue
-        if first_iter:
-            first_iter = False
-
-    if last_seq_code == 'i':
-        if last_seq.upper() == alt_base.upper():
-            counts[3] += 1
-            if forward_flag:
-                counts[4] += 1
-            else:
-                counts[5] += 1
-        else:
-            counts[6] += 1
-            if forward_flag:
-                counts[7] += 1
-            else:
-                counts[8] += 1
-    elif last_seq_code == 'd':
-        if last_seq.upper() == ref_base.upper():
-            counts[3] += 1
-            if forward_flag:
-                counts[4] += 1
-            else:
-                counts[5] += 1
-        else:
-            counts[6] += 1
-            if forward_flag:
-                counts[7] += 1
-            else:
-                counts[8] += 1
-    elif last_seq_code == 'b':
-        if last_seq.upper() == ref_base.upper():
-            counts[0] += 1
-            if forward_flag:
-                counts[1] += 1
-            else:
-                counts[2] += 1
-        elif last_seq.upper() == alt_base.upper():
-            counts[3] += 1
-            if forward_flag:
-                counts[4] += 1
-            else:
-                counts[5] += 1
-        else:
-            counts[6] += 1
-            if forward_flag:
-                counts[7] += 1
-            else:
-                counts[8] += 1
-    dp = int(fields[3])
-    if sum([counts[0], counts[3], counts[6]]) == 0:
-        af = float("nan")
-    else:
-        af = float(counts[3]) / float(sum([counts[0], counts[3], counts[6]]))
-    if sum([counts[1], counts[4], counts[7]]) == 0:
-        faf = float("nan")
-    else:
-        faf = float(counts[4]) / float(sum([counts[1], counts[4], counts[7]]))
-    if sum([counts[2], counts[5], counts[8]]) == 0:
-        raf = float("nan")
-    else:
-        raf = float(counts[5]) / float(sum([counts[2], counts[5], counts[8]]))
-    dp4 = [counts[1], counts[2], counts[4], counts[5]]
-    return (dp, af, faf, raf, dp4)
-
-
-def annotateVCF(in_vcf_filepath, in_mpileup_filepath, out_vcf_filepath):
-    in_vcf = open(in_vcf_filepath, 'r')
-    in_mpileup = open(in_mpileup_filepath, 'r')
-    out_vcf = open(out_vcf_filepath, 'w')
-
-    # First pass parsing of input vcf, output headerlines + new headerlines, add VCF sites we care about to to_examine (limits memory usage for sites that don't need annotation)
-    to_examine = {}
-    for line in in_vcf:
-        if line[0:2] == "##":
-            out_vcf.write(line)
-        elif line[0] == "#":
-            out_vcf.write("##annotateVCFVersion=0.2\n")
-            out_vcf.write("##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Raw Depth\">\n")
-            out_vcf.write("##INFO=<ID=AF,Number=1,Type=Float,Description=\"Allele Frequency\">\n")
-            out_vcf.write("##INFO=<ID=FAF,Number=1,Type=Float,Description=\"Forward Allele Frequency\">\n")
-            out_vcf.write("##INFO=<ID=RAF,Number=1,Type=Float,Description=\"Reverse Allele Frequency\">\n")
-            out_vcf.write("##INFO=<ID=SB,Number=1,Type=Integer,Description=\"Phred-scaled strand bias at this position\">\n")
-            out_vcf.write("##INFO=<ID=DP4,Number=4,Type=Integer,Description=\"Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\n")
-            out_vcf.write(line)
-        else:
-            fields = line.strip().split()
-            if fields[0] in to_examine:
-                to_examine[fields[0]][int(fields[1])] = (fields[3], fields[4])
-            else:
-                to_examine[fields[0]] = {int(fields[1]): (fields[3], fields[4])}
-    in_vcf.close()
-    data = {}
-
-    # Populate data dictionary, which relates chromosome and position to the following:
-    #  depth of coverage
-    #  allele frequency
-    #  forward strand allele frequency
-    #  reverse strand allele frequency
-    #  dp4 - depth of coverage of ref allele fwd strand, DOC of ref allele rev strand, DOC of alt allele fwd strand, DOC of alt allele rev strand
-    for line in in_mpileup:
-        fields = line.strip().split()
-        if fields[0] not in to_examine:
-            continue
-        if int(fields[1]) not in to_examine[fields[0]]:
-            continue
-        (ref_base, alt_base) = to_examine[fields[0]][int(fields[1])]
-        if len(ref_base.split(',')) > 1:  # Can't handle multiple ref alleles
-            continue
-        if len(alt_base.split(',')) > 1:  # Can't handle multiple alt alleles
-            continue
-        if len(ref_base) > 1 or len(alt_base) > 1:
-            if len(ref_base) > 1 and len(alt_base) > 1:  # Can't handle complex indels
-                continue
-            data[(fields[0], int(fields[1]))] = parseIndelPileup(fields, ref_base, alt_base)
-        if len(ref_base) == 1 and len(alt_base) == 1:
-            data[(fields[0], int(fields[1]))] = parseSimpleSNPpileup(fields, ref_base, alt_base)
-    in_mpileup.close()
-    # Reopen vcf, this time, skip header, annotate all the sites for which there is an entry in data dictionary
-    # (Sites without entries have either multiple ref or alt bases, or have complex indels. Not supported (for now), and not reported as a result)
-    in_vcf = open(in_vcf_filepath, 'r')
-    for line in in_vcf:
-        if line[0] == '#':
-            continue
-        fields = line.strip().split('\t')
-        if (fields[0], int(fields[1])) not in data:
-            continue
-        (dp, af, faf, raf, dp4) = data[(fields[0], int(fields[1]))]
-        dp2x2 = [[dp4[0], dp4[1]], [dp4[2], dp4[3]]]
-        _, p_val = fisher_exact(dp2x2)
-        sb = pval_to_phredqual(p_val)
-        if fields[7] == "":
-            info = []
-        else:
-            info = fields[7].split(';')
-        info.append("DP=%d" % (dp))
-        if isnan(af):
-            info.append("AF=NaN")
-        else:
-            info.append("AF=%.6f" % (af))
-        if isnan(faf):
-            info.append("FAF=NaN")
-        else:
-            info.append("FAF=%.6f" % (faf))
-        if isnan(raf):
-            info.append("RAF=NaN")
-        else:
-            info.append("RAF=%.6f" % (raf))
-        info.append("SB=%d" % (sb))
-        info.append("DP4=%s" % (','.join([str(x) for x in dp4])))
-        new_info = ';'.join(info)
-        fields[7] = new_info
-        out_vcf.write("%s\n" % ("\t".join(fields)))
-    in_vcf.close()
-    out_vcf.close()
-
-
-if __name__ == "__main__":
-    annotateVCF(sys.argv[1], sys.argv[2], sys.argv[3])
diff -r a7228a7ea146 -r 1ca4ce7241fd convert_VCF_info_fields.py
--- a/convert_VCF_info_fields.py	Mon Mar 29 20:06:44 2021 +0000
+++ b/convert_VCF_info_fields.py	Thu Apr 22 20:25:13 2021 +0000
@@ -11,7 +11,8 @@
 from collections import OrderedDict
 from math import log10
 
-from scipy.stats import fisher_exact
+import scipy
+import scipy.stats
 
 
 def pval_to_phredqual(pval):
@@ -69,7 +70,7 @@
                 for j, i in enumerate(range(2, len(sr_list), 2)):
                     dp4 = (sr_list[ref_fwd], sr_list[ref_rev], sr_list[i], sr_list[i + 1])
                     dp2x2 = [[dp4[0], dp4[1]], [dp4[2], dp4[3]]]
-                    _, p_val = fisher_exact(dp2x2)
+                    _, p_val = scipy.stats.fisher_exact(dp2x2)
                     sb = pval_to_phredqual(p_val)
 
                     as_ = (sc_list[ref_fwd], sc_list[ref_rev], sc_list[i], sc_list[i + 1])
diff -r a7228a7ea146 -r 1ca4ce7241fd macros.xml
--- a/macros.xml	Mon Mar 29 20:06:44 2021 +0000
+++ b/macros.xml	Thu Apr 22 20:25:13 2021 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">1.0.3</token>
-    <token name="@PROFILE@">18.01</token>
+    <token name="@TOOL_VERSION@">1.3.2</token>
+    <token name="@PROFILE@">20.01</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">medaka</requirement>
@@ -48,29 +48,32 @@
     </xml>
     <xml name="model" token_argument="-m" token_label="Select model">
         <param argument="@ARGUMENT@" type="select" label="@LABEL@">
-            <option value="r10_min_high_g303">r10_min_high_g303</option>
-            <option value="r10_min_high_g340">r10_min_high_g340</option>
             <option value="r103_min_high_g345">r103_min_high_g345</option>
             <option value="r103_min_high_g360">r103_min_high_g360</option>
             <option value="r103_prom_high_g360">r103_prom_high_g360</option>
             <option value="r103_prom_snp_g3210">r103_prom_snp_g3210</option>
             <option value="r103_prom_variant_g3210">r103_prom_variant_g3210</option>
+            <option value="r10_min_high_g303">r10_min_high_g303</option>
+            <option value="r10_min_high_g340">r10_min_high_g340</option>
             <option value="r941_min_fast_g303">r941_min_fast_g303</option>
             <option value="r941_min_high_g303">r941_min_high_g303</option>
             <option value="r941_min_high_g330">r941_min_high_g330</option>
             <option value="r941_min_high_g340_rle">r941_min_high_g340_rle</option>
             <option value="r941_min_high_g344">r941_min_high_g344</option>
             <option value="r941_min_high_g351">r941_min_high_g351</option>
-            <option value="r941_min_high_g360">r941_min_high_g360</option>
+            <option value="r941_min_high_g360" selected="true">r941_min_high_g360</option>
             <option value="r941_prom_fast_g303">r941_prom_fast_g303</option>
             <option value="r941_prom_high_g303">r941_prom_high_g303</option>
             <option value="r941_prom_high_g330">r941_prom_high_g330</option>
             <option value="r941_prom_high_g344">r941_prom_high_g344</option>
-            <option value="r941_prom_high_g360" selected="true">r941_prom_high_g360</option>
+            <option value="r941_prom_high_g360">r941_prom_high_g360</option>
+            <option value="r941_prom_high_g4011">r941_prom_high_g4011</option>
             <option value="r941_prom_snp_g303">r941_prom_snp_g303</option>
             <option value="r941_prom_snp_g322">r941_prom_snp_g322</option>
+            <option value="r941_prom_snp_g360">r941_prom_snp_g360</option>
             <option value="r941_prom_variant_g303">r941_prom_variant_g303</option>
             <option value="r941_prom_variant_g322">r941_prom_variant_g322</option>
+            <option value="r941_prom_variant_g360">r941_prom_variant_g360</option>
         </param>
     </xml>
     <xml name="reference">
diff -r a7228a7ea146 -r 1ca4ce7241fd medaka_consensus.xml
--- a/medaka_consensus.xml	Mon Mar 29 20:06:44 2021 +0000
+++ b/medaka_consensus.xml	Thu Apr 22 20:25:13 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="medaka_consensus_pipeline" name="medaka consensus pipeline" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
+<tool id="medaka_consensus_pipeline" name="medaka consensus pipeline" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>Assembly polishing via neural networks</description>
     <macros>
         <import>macros.xml</import>
@@ -11,9 +11,6 @@
 -m ${m}
 -b $b
 -o results
-#if 'draft' in str($out).split(',') or 'variants' in str($out).split(',') or 'polished' in str($out).split(',')
-    -v
-#end if
 -t \${GALAXY_SLOTS:-4}
 ## required
 -i '$i'
@@ -26,14 +23,13 @@
         <param argument="-d" type="data" format="fasta,fasta.gz" label="Select assembly" help="The input assembly should be preprocessed with racon."/>
         <expand macro="model"/>
         <expand macro="b"/>
+        <param argument="-g" type="boolean" truevalue="-g" falsevalue="" label="Don't fill gaps in consensus with draft sequence?" checked="false" />
         <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)" help="'Draft To Consensus', 'Variants' and 'Polished regions in draft coordinates' are generated using the parameter -v.">
             <option value="consensus" selected="true">Consensus</option>
             <option value="probs" selected="true">Consensus probabilities</option>
             <option value="calls" selected="true">Calls to draft</option>
-            <option value="draft">Draft to consensus</option>
-            <option value="variants">Variants</option>
-            <option value="polished">Polished regions in draft coordinates</option>
             <option value="log">Log</option>
+            <option value="gaps">Gap regions in draft</option>
         </param>
     </inputs>
     <outputs>
@@ -47,15 +43,8 @@
         <data name="out_calls" format="bam" from_work_dir="results/calls_to_draft.bam" label="${tool.name} on ${on_string}: Calls to draft">
             <filter>'calls' in out</filter>
         </data>
-        <!-- optional with parameter -v -->
-        <data name="out_draft" format="txt" from_work_dir="results/draft_to_consensus.chain" label="${tool.name} on ${on_string}: Draft to consensus">
-            <filter>'draft' in out</filter>
-        </data>
-        <data name="out_variants" format="vcf_bgzip" from_work_dir="results/variants.vcf.gz" label="${tool.name} on ${on_string}: Variants">
-            <filter>'variants' in out</filter>
-        </data>
-        <data name="out_polished" format="bed" from_work_dir="results/polished_regions_in_draft_coords.bed" label="${tool.name} on ${on_string}: Polished regions in Draft">
-            <filter>'polished' in out</filter>
+        <data name="out_gaps" format="bed" from_work_dir="results/consensus.fasta.gaps_in_draft_coords.bed" label="${tool.name} on ${on_string}: Gaps in draft">
+            <filter>'gaps' in out</filter>
         </data>
         <!-- optional -->
         <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
@@ -70,13 +59,13 @@
             <output name="out_consensus">
                 <assert_contents>
                     <has_n_lines n="2"/>
-                    <has_line line=">4_segment0 4:1.0-3792.0"/>
+                    <has_line line=">4"/>
                     <has_text_matching expression=".+GTCAGAATCGCGTTCAGCGCGTTTCAGCGGTGCGTACAATT.+"/>
                 </assert_contents>
             </output>
             <output name="out_probs">
                 <assert_contents>
-                    <has_size value="165271" delta="100"/>
+                    <has_size value="165503" delta="100"/>
                 </assert_contents>
             </output>
             <output name="out_calls">
@@ -86,17 +75,16 @@
             </output>
         </test>
         <!-- #2 -->
-        <test expect_num_outputs="7">
+        <test expect_num_outputs="5">
             <param name="i" value="basecalls.fastq"/>
             <param name="d" value="assembly.fasta"/>
             <param name="m" value="r941_min_fast_g303"/>
             <param name="b" value="99"/>
-            <param name="out" value="consensus,probs,calls,draft,variants,polished,log"/>
+            <param name="out" value="consensus,probs,calls,log,gaps"/>
             <output name="out_consensus">
                 <assert_contents>
-                    <has_n_lines n="65"/>
-                    <has_line line=">4 length=3792 depth=114.52x circular=true"/>
-                    <has_line line="ATCTCTTT"/>
+                    <has_n_lines n="2"/>
+                    <has_line line=">4"/> <!-- Replace test -->
                 </assert_contents>
             </output>
             <output name="out_probs">
@@ -109,27 +97,16 @@
                     <has_size value="343197" delta="100"/>
                 </assert_contents>
             </output>
-            <output name="out_draft">
-                <assert_contents>
-                    <has_line line="chain 3788 4 3792 + 0 3792 4 3788 + 0 3788 1"/>
-                    <has_line line="1409 1 0"/>
-                    <has_line line="440 1 0"/>
-                    <has_line line="736 1 0"/>
-                    <has_line line="853 1 0"/>
-                    <has_line line="350"/>
-                </assert_contents>
-            </output>
-            <output name="out_polished">
-                <assert_contents>
-                    <has_size value="9"/>
-                </assert_contents>
-            </output>
-            <output name="out_variants" file="variants.vcf.gz" decompress="true"/>
             <output name="out_log">
                 <assert_contents>
                     <has_line line="Polished assembly written to results/consensus.fasta, have a nice day."/>
                 </assert_contents>
             </output>
+            <output name="out_gaps">
+                <assert_contents>
+                    <has_size value="0" delta="0"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[
diff -r a7228a7ea146 -r 1ca4ce7241fd test-data/all_fasta.loc
--- a/test-data/all_fasta.loc	Mon Mar 29 20:06:44 2021 +0000
+++ b/test-data/all_fasta.loc	Thu Apr 22 20:25:13 2021 +0000
@@ -1,1 +1,1 @@
-bwa-mem-mt-genome	bwa-mem-mt-genome	bwa-mem-mt-genome	${__HERE__}/bwa-mem-mt-genome.fa
\ No newline at end of file
+ref_fasta	ref_fasta	ref_fasta	${__HERE__}/ref.fasta
\ No newline at end of file
diff -r a7228a7ea146 -r 1ca4ce7241fd test-data/bwa-mem-mt-genome.fa
--- a/test-data/bwa-mem-mt-genome.fa	Mon Mar 29 20:06:44 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,238 +0,0 @@
->gi|251831106|ref|NC_012920.1|
-GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG
-GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC
-CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA
-ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC
-ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA
-AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC
-TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA
-CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC
-AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC
-ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA
-GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC
-AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA
-ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA
-TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACT
-CACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC
-ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC
-AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC
-CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA
-CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC
-AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT
-GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGA
-AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA
-TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA
-GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA
-GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG
-ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA
-ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCC
-AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA
-AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGAT
-AGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC
-CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG
-TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC
-ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG
-TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC
-AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA
-AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC
-ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA
-AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT
-TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA
-TGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT
-AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG
-TCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA
-GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG
-ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG
-AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT
-ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGA
-ACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAAT
-TCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA
-TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCC
-CCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC
-ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCC
-CTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG
-CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGC
-AGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC
-TCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGG
-CCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCTTCGACCTTGCCGAAGGGGAGTC
-CGAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAGGCCCCTTCGCCCTATTCTTCATAGCCGAATAC
-ACAAACATTATTATAATAAACACCCTCACCACTACAATCTTCCTAGGAACAACATATGACGCACTCTCCC
-CTGAACTCTACACAACATATTTTGTCACCAAGACCCTACTTCTAACCTCCCTGTTCTTATGAATTCGAAC
-AGCATACCCCCGATTCCGCTACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCCTA
-GCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCCCCCTCAAACCTAAGAAATAT
-GTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACCCCCTTATTTCTAGGACTATGA
-GAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAAGTAAGGTC
-AGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAATTAATCCCCT
-GGCCCAACCCGTCATCTACTCTACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTT
-TTTACCTGAGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTCTAACCAAAAAAATAAACCCTC
-GTTCCACAGAAGCTGCCATCAAGTATTTCCTCACGCAAGCAACCGCATCCATAATCCTTCTAATAGCTAT
-CCTCTTCAACAATATACTCTCCGGACAATGAACCATAACCAATACTACCAATCAATACTCATCATTAATA
-ATCATAATAGCTATAGCAATAAAACTAGGAATAGCCCCCTTTCACTTCTGAGTCCCAGAGGTTACCCAAG
-GCACCCCTCTGACATCCGGCCTGCTTCTTCTCACATGACAAAAACTAGCCCCCATCTCAATCATATACCA
-AATCTCTCCCTCACTAAACGTAAGCCTTCTCCTCACTCTCTCAATCTTATCCATCATAGCAGGCAGTTGA
-GGTGGATTAAACCAAACCCAGCTACGCAAAATCTTAGCATACTCCTCAATTACCCACATAGGATGAATAA
-TAGCAGTTCTACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTATCCTAACTACTAC
-CGCATTCCTACTACTCAACTTAAACTCCAGCACCACGACCCTACTACTATCTCGCACCTGAAACAAGCTA
-ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCTGCCCCCGCTAACCGGCTTTT
-TGCCCAAATGGGCCATTATCGAAGAATTCACAAAAAACAATAGCCTCATCATCCCCACCATCATAGCCAC
-CATCACCCTCCTTAACCTCTACTTCTACCTACGCCTAATCTACTCCACCTCAATCACACTACTCCCCATA
-TCTAACAACGTAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCCCACACTCATCG
-CCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATACTAATAATCTTATAGAAATTTAGGTTAAATAC
-AGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTGTAACAGCTAAGGACTGCAAAA
-CCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTACTAGACCAATGGGA
-CTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCC
-GCCGGGAAAAAAGGCGGGAGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGA
-AAATCACCTCGGAGCTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCACTCA
-GCCATTTTACCTCACCCCCACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCACAAAGACATTGG
-AACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCTCTAAGCCTCCTTATTCGAGCC
-GAGCTGGGCCAGCCAGGCAACCTTCTAGGTAACGACCACATCTACAACGTTATCGTCACAGCCCATGCAT
-TTGTAATAATCTTCTTCATAGTAATACCCATCATAATCGGAGGCTTTGGCAACTGACTAGTTCCCCTAAT
-AATCGGTGCCCCCGATATGGCGTTTCCCCGCATAAACAACATAAGCTTCTGACTCTTACCTCCCTCTCTC
-CTACTCCTGCTCGCATCTGCTATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTTAG
-CAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTTACACCTAGCAGGTGTCTC
-CTCTATCTTAGGGGCCATCAATTTCATCACAACAATTATCAATATAAAACCCCCTGCCATAACCCAATAC
-CAAACGCCCCTCTTCGTCTGATCCGTCCTAATCACAGCAGTCCTACTTCTCCTATCTCTCCCAGTCCTAG
-CTGCTGGCATCACTATACTACTAACAGACCGCAACCTCAACACCACCTTCTTCGACCCCGCCGGAGGAGG
-AGACCCCATTCTATACCAACACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACCA
-GGCTTCGGAATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAGAACCATTTGGATACATAGGTA
-TGGTCTGAGCTATGATATCAATTGGCTTCCTAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGG
-AATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCACCGGCGTCAAA
-GTATTTAGCTGACTCGCCACACTCCACGGAAGCAATATGAAATGATCTGCTGCAGTGCTCTGAGCCCTAG
-GATTCATCTTTCTTTTCACCGTAGGTGGCCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGT
-ACTACACGACACGTACTACGTTGTAGCCCACTTCCACTATGTCCTATCAATAGGAGCTGTATTTGCCATC
-ATAGGAGGCTTCATTCACTGATTTCCCCTATTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAATCC
-ATTTCACTATCATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGGCCTATCCGGAAT
-GCCCCGACGTTACTCGGACTACCCCGATGCATACACCACATGAAACATCCTATCATCTGTAGGCTCATTC
-ATTTCTCTAACAGCAGTAATATTAATAATTTTCATGATTTGAGAAGCCTTCGCTTCGAAGCGAAAAGTCC
-TAATAGTAGAAGAACCCTCCATAAACCTGGAGTGACTATATGGATGCCCCCCACCCTACCACACATTCGA
-AGAACCCGTATACATAAAATCTAGACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAA
-CCCCATGGCCTCCATGACTTTTTCAAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAAT
-TATAGGCTAAATCCTATATATCTTAATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCT
-ATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCC
-TGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATCTCAGACGCTCAGGAAATAGA
-AACCGTCTGAACTATCCTGCCCGCCATCATCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTAC
-ATAACAGACGAGGTCAACGATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACG
-AGTACACCGACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGCGA
-CCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACA
-TCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAACAGATGCAATTCCCGGACGTC
-TAAACCAAACCACTTTCACCGCTACACGACCGGGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGC
-AAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATAGGGCCCGTATTT
-ACCCTATAGCACCCCCTCTACCCCCTCTAGAGCCCACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTT
-AAAGATTAAGAGAACCAACACCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACCAT
-AATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATATTAAACACAAACTACCACCTA
-CCTCCCTCACCAAAGCCCATAAAAATAAAAAATTATAACAAACCCTGAGAACCAAAATGAACGAAAATCT
-GTTCGCTTCATTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCAGTACTGATCATTCTATTTCCCCCT
-CTATTGATCCCCACCTCCAAATATCTCATCAACAACCGACTAATCACCACCCAACAATGACTAATCAAAC
-TAACCTCAAAACAAATGATAACCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTT
-AATCATTTTTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCATTTACACCAACCACCCAACTA
-TCTATAAACCTAGCCATGGCCATCCCCTTATGAGCGGGCACAGTGATTATAGGCTTTCGCTCTAAGATTA
-AAAATGCCCTAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTATCCCCATACTAGTTATTATCGA
-AACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTACGCCTAACCGCTAACATTACTGCAGGCCAC
-CTACTCATGCACCTAATTGGAAGCGCCACCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCA
-TCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCTTAATCCAAGCCTACGTTTTCAC
-ACTTCTAGTAAGCCTCTACCTGCACGACAACACATAATGACCCACCAATCACATGCCTATCATATAGTAA
-AACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTAGCCATGTGATT
-TCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTAACCAACACACTAACCATATACCAATGATGG
-CGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATACG
-GGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTTCTGAGCCTTTTACCACTCCAG
-CCTAGCCCCTACCCCCCAATTAGGAGGGCACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAA
-GTCCCACTCCTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCACCATAGTCTAA
-TAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTATTACAATTTTACTGGGTCTCTATTTTACCCT
-CCTACAAGCCTCAGAGTACTTCGAGTCTCCCTTCACCATTTCCGACGGCATCTACGGCTCAACATTTTTT
-GTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGGCTCAACTTTCCTCACTATCTGCTTCATCCGCC
-AACTAATATTTCACTTTACATCCAAACATCACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGT
-AGATGTGGTTTGACTATTTCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTAGTATAAATAGT
-ACCGTTAACTTCCAATTAACTAGTTTTGACAACATTCAAAAAAGAGTAATAAACTTCGCCTTAATTTTAA
-TAATCAACACCCTCCTAGCCTTACTACTAATAATTATTACATTTTGACTACCACAACTCAACGGCTACAT
-AGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGCCCGCGTCCCTTTCTCCATAAAA
-TTCTTCTTAGTAGCTATTACCTTCTTATTATTTGATCTAGAAATTGCCCTCCTTTTACCCCTACCATGAG
-CCCTACAAACAACTAACCTGCCACTAATAGTTATGTCATCCCTCTTATTAATCATCATCCTAGCCCTAAG
-TCTGGCCTATGAGTGACTACAAAAAGGATTAGACTGAACCGAATTGGTATATAGTTTAAACAAAACGAAT
-GATTTCGACTCATTAAATTATGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACTAG
-CATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATATCCTCCCTACTATGCCTAGA
-AGGAATAATACTATCGCTGTTCATTATAGCTACTCTCATAACCCTCAACACCCACTCCCTCTTAGCCAAT
-ATTGTGCCTATTGCCATACTAGTCTTTGCCGCCTGCGAAGCAGCGGTGGGCCTAGCCCTACTAGTCTCAA
-TCTCCAACACATATGGCCTAGACTACGTACATAACCTAAACCTACTCCAATGCTAAAACTAATCGTCCCA
-ACAATTATATTACTACCACTGACATGACTTTCCAAAAAACACATAATTTGAATCAACACAACCACCCACA
-GCCTAATTATTAGCATCATCCCTCTACTATTTTTTAACCAAATCAACAACAACCTATTTAGCTGTTCCCC
-AACCTTTTCCTCCGACCCCCTAACAACCCCCCTCCTAATACTAACTACCTGACTCCTACCCCTCACAATC
-ATGGCAAGCCAACGCCACTTATCCAGTGAACCACTATCACGAAAAAAACTCTACCTCTCTATACTAATCT
-CCCTACAAATCTCCTTAATTATAACATTCACAGCCACAGAACTAATCATATTTTATATCTTCTTCGAAAC
-CACACTTATCCCCACCTTGGCTATCATCACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACA
-TACTTCCTATTCTACACCCTAGTAGGCTCCCTTCCCCTACTCATCGCACTAATTTACACTCACAACACCC
-TAGGCTCACTAAACATTCTACTACTCACTCTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAACTT
-AATATGACTAGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCACTTATGACTCCCT
-AAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTACTTGCCGCAGTACTCTTAAAACTAGGCGGCT
-ATGGTATAATACGCCTCACACTCATTCTCAACCCCCTGACAAAACACATAGCCTACCCCTTCCTTGTACT
-ATCCCTATGAGGCATAATTATAACAAGCTCCATCTGCCTACGACAAACAGACCTAAAATCGCTCATTGCA
-TACTCTTCAATCAGCCACATAGCCCTCGTAGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCG
-GCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTA
-CGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTT
-TGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTG
-TGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGC
-CCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAA
-CCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACC
-CCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAA
-CAGAGGCTTACGACCCCTTATTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCCCCCATGTCTAAC
-AACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCA
-ACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCC
-ATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCAT
-CCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAA
-CTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAATA
-TTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACTGTGATATATAAACTCAGACC
-CAAACATTAATCAGTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAA
-CAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGA
-TACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT
-TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA
-CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT
-CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTA
-TAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC
-TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATC
-AAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC
-CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTC
-CATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC
-ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCA
-AAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGC
-TACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC
-ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC
-TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTA
-CCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC
-AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCA
-TCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT
-AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCA
-ACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAA
-TCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAA
-CTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA
-CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC
-TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCC
-CTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCC
-CCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG
-ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACC
-CCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC
-CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAAC
-CCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA
-ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTA
-CTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATC
-ATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC
-TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC
-AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAAC
-TTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACA
-GTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACT
-CCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC
-ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACAT
-TAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC
-TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTA
-GGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC
-AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT
-AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATAC
-TTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTC
-CTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA
-GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTC
-ATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA
-TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA
-ATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA
-ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAG
-TACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC
-TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG
-CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC
-ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG
diff -r a7228a7ea146 -r 1ca4ce7241fd test-data/bwa-mem-mt-genome.fa.fai
--- a/test-data/bwa-mem-mt-genome.fa.fai	Mon Mar 29 20:06:44 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-gi|251831106|ref|NC_012920.1|	16569	31	70	71