# HG changeset patch # User iuc # Date 1619123135 0 # Node ID 9fb05560464801c65360d182f369df0edf1d4b39 # Parent 43815fa60f3ad101b02b8bed255237b4427f6dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13" diff -r 43815fa60f3a -r 9fb055604648 annotateVCF.py --- a/annotateVCF.py Mon Mar 29 20:05:39 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=\n") - out_vcf.write("##INFO=\n") - out_vcf.write("##INFO=\n") - out_vcf.write("##INFO=\n") - out_vcf.write("##INFO=\n") - out_vcf.write("##INFO=\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 43815fa60f3a -r 9fb055604648 convert_VCF_info_fields.py --- a/convert_VCF_info_fields.py Mon Mar 29 20:05:39 2021 +0000 +++ b/convert_VCF_info_fields.py Thu Apr 22 20:25:35 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 43815fa60f3a -r 9fb055604648 macros.xml --- a/macros.xml Mon Mar 29 20:05:39 2021 +0000 +++ b/macros.xml Thu Apr 22 20:25:35 2021 +0000 @@ -1,7 +1,7 @@ - 1.0.3 - 18.01 + 1.3.2 + 20.01 medaka @@ -48,29 +48,32 @@ - - + + - + - + + + + diff -r 43815fa60f3a -r 9fb055604648 test-data/all_fasta.loc --- a/test-data/all_fasta.loc Mon Mar 29 20:05:39 2021 +0000 +++ b/test-data/all_fasta.loc Thu Apr 22 20:25:35 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 43815fa60f3a -r 9fb055604648 test-data/bwa-mem-mt-genome.fa --- a/test-data/bwa-mem-mt-genome.fa Mon Mar 29 20:05:39 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 43815fa60f3a -r 9fb055604648 test-data/bwa-mem-mt-genome.fa.fai --- a/test-data/bwa-mem-mt-genome.fa.fai Mon Mar 29 20:05:39 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 diff -r 43815fa60f3a -r 9fb055604648 variant.xml --- a/variant.xml Mon Mar 29 20:05:39 2021 +0000 +++ b/variant.xml Thu Apr 22 20:25:35 2021 +0000 @@ -1,12 +1,10 @@ - + Probability decoding macros.xml - - scipy - + @@ -39,13 +37,14 @@ --regions '${regions}' #end if $verbose + ${ambig_ref} + ${gvcf} ## required reference.fa #for $current in $pool.inputs '$current' #end for '$out_result' ## output - 2>&1 | tee '$out_log' #elif $pool.pool_mode == "No": ## run @@ -56,26 +55,27 @@ --regions '${regions}' #end if $verbose + ${ambig_ref} + ${gvcf} ## required reference.fa '$pool.input' '$out_result' ##output 2>&1 | tee '$out_log' #end if - #if $out_annotated: ## medaka annotate errors out if the reference is lower case at a position it's annotating because it checks vs the ref base in the vcf && python '$convert_fasta' reference.fa upper_reference.fa && ln -s '$output_annotated.in_bam' in.bam && ln -s '$output_annotated.in_bam.metadata.bam_index' in.bai - && medaka tools annotate --pad $output_annotated.pad '$out_result' upper_reference.fa in.bam tmp.vcf - && '$__tool_directory__/convert_VCF_info_fields.py' tmp.vcf '$out_annotated' + && medaka tools annotate --dpsp --pad $output_annotated.pad '$out_result' upper_reference.fa in.bam tmp.vcf + && python '$__tool_directory__/convert_VCF_info_fields.py' tmp.vcf '$out_annotated' #end if ]]> - + @@ -96,6 +96,8 @@ + + @@ -129,8 +131,9 @@ - + + @@ -146,7 +149,7 @@ - + @@ -168,6 +171,7 @@ + @@ -183,7 +187,7 @@ - +