| Previous changeset 1:3556001ff2db (2019-12-04) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468" |
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modified:
mut2read.py mut2read.xml mut2sscs.py mut2sscs.xml read2mut.py read2mut.xml va_macros.xml |
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added:
test-data/Aligned_Families_test.tabular test-data/DCS_test.bam test-data/DCS_test.bam.bai test-data/FreeBayes_test.vcf test-data/Interesting_Reads_test.fastq test-data/Interesting_Reads_test.trim.bai test-data/Interesting_Reads_test.trim.bam test-data/Interesting_Reads_test.trim.fastq test-data/Interesting_Reads_test.trim.log test-data/SSCS_counts_test.json test-data/SSCS_test.bam test-data/SSCS_test.bam.bai test-data/Variant_Analyzer_test.xlsx test-data/reference.fasta test-data/tag_count_dict_test.json |
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removed:
test-data/Aligned_Families_test_data_VA.tabular test-data/DCS_Mutations_test_data_VA.tabular test-data/DCS_test_data_VA.bam test-data/DCS_test_data_VA.bam.bai test-data/Interesting_Reads_test_data_VA.fastq test-data/Interesting_Reads_test_data_VA.trim.bam test-data/Interesting_Reads_test_data_VA.trim.bam.bai test-data/SSCS_counts_test_data_VA.json test-data/SSCS_test_data_VA.bam test-data/SSCS_test_data_VA.bam.bai test-data/mutant_reads_summary_short_trim_test_data_VA.xlsx test-data/tag_count_dict_test_data_VA.json |
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| diff -r 3556001ff2db -r 3f1dbd2c59bf mut2read.py --- a/mut2read.py Wed Dec 04 16:21:17 2019 -0500 +++ b/mut2read.py Tue Nov 10 12:55:29 2020 +0000 |
| [ |
| @@ -11,11 +11,10 @@ ======= ========== ================= ================================ Version Date Author Description -0.2.1 2019-10-27 Gundula Povysil - +2.0.0 2020-10-30 Gundula Povysil - ======= ========== ================= ================================ -USAGE: python mut2read.py DCS_Mutations.tabular DCS.bam Aligned_Families.tabular Interesting_Reads.fastq - tag_count_dict.json +USAGE: python mut2read.py DCS_Mutations.tabular DCS.bam Aligned_Families.tabular Interesting_Reads.fastq tag_count_dict.json """ import argparse @@ -25,12 +24,13 @@ import numpy as np import pysam +from cyvcf2 import VCF def make_argparser(): - parser = argparse.ArgumentParser(description='Takes a tabular file with mutations and a BAM file as input and prints all tags of reads that carry the mutation to a user specified output file and creates a fastq file of reads of tags with mutation.') + parser = argparse.ArgumentParser(description='Takes a vcf file with mutations and a BAM file as input and prints all tags of reads that carry the mutation to a user specified output file and creates a fastq file of reads of tags with mutation.') parser.add_argument('--mutFile', - help='TABULAR file with DCS mutations.') + help='VCF file with DCS mutations.') parser.add_argument('--bamFile', help='BAM file with aligned DCS reads.') parser.add_argument('--familiesFile', @@ -61,71 +61,62 @@ if os.path.isfile(file3) is False: sys.exit("Error: Could not find '{}'".format(file3)) - # read mut file - with open(file1, 'r') as mut: - mut_array = np.genfromtxt(mut, skip_header=1, delimiter='\t', comments='#', dtype=str) - # read dcs bam file - # pysam.index(file2) bam = pysam.AlignmentFile(file2, "rb") # get tags tag_dict = {} cvrg_dict = {} - if len(mut_array) == 13: - mut_array = mut_array.reshape((1, len(mut_array))) - - for m in range(len(mut_array[:, 0])): - print(str(m + 1) + " of " + str(len(mut_array[:, 0]))) - chrom = mut_array[m, 1] - stop_pos = mut_array[m, 2].astype(int) + for variant in VCF(file1): + chrom = variant.CHROM + stop_pos = variant.start chrom_stop_pos = str(chrom) + "#" + str(stop_pos) - ref = mut_array[m, 9] - alt = mut_array[m, 10] - + ref = variant.REF + alt = variant.ALT[0] dcs_len = [] - - for pileupcolumn in bam.pileup(chrom, stop_pos - 2, stop_pos, max_depth=100000000): + if len(ref) == len(alt): + for pileupcolumn in bam.pileup(chrom, stop_pos - 1, stop_pos + 1, max_depth=100000000): + if pileupcolumn.reference_pos == stop_pos: + count_alt = 0 + count_ref = 0 + count_indel = 0 + count_n = 0 + count_other = 0 + count_lowq = 0 + print("unfiltered reads=", pileupcolumn.n, "filtered reads=", len(pileupcolumn.pileups), + "difference= ", len(pileupcolumn.pileups) - pileupcolumn.n) + for pileupread in pileupcolumn.pileups: + if not pileupread.is_del and not pileupread.is_refskip: + # query position is None if is_del or is_refskip is set. + nuc = pileupread.alignment.query_sequence[pileupread.query_position] + dcs_len.append(len(pileupread.alignment.query_sequence)) + if nuc == alt: + count_alt += 1 + tag = pileupread.alignment.query_name + if tag in tag_dict: + tag_dict[tag][chrom_stop_pos] = alt + else: + tag_dict[tag] = {} + tag_dict[tag][chrom_stop_pos] = alt + elif nuc == ref: + count_ref += 1 + elif nuc == "N": + count_n += 1 + elif nuc == "lowQ": + count_lowq += 1 + else: + count_other += 1 + else: + count_indel += 1 + dcs_median = np.median(np.array(dcs_len)) + cvrg_dict[chrom_stop_pos] = (count_ref, count_alt, dcs_median) - if pileupcolumn.reference_pos == stop_pos - 1: - count_alt = 0 - count_ref = 0 - count_indel = 0 - count_n = 0 - count_other = 0 - count_lowq = 0 - print("unfiltered reads=", pileupcolumn.n, "filtered reads=", len(pileupcolumn.pileups), - "difference= ", len(pileupcolumn.pileups) - pileupcolumn.n) - for pileupread in pileupcolumn.pileups: - if not pileupread.is_del and not pileupread.is_refskip: - # query position is None if is_del or is_refskip is set. - nuc = pileupread.alignment.query_sequence[pileupread.query_position] - dcs_len.append(len(pileupread.alignment.query_sequence)) - if nuc == alt: - count_alt += 1 - tag = pileupread.alignment.query_name - if tag in tag_dict: - tag_dict[tag][chrom_stop_pos] = alt - else: - tag_dict[tag] = {} - tag_dict[tag][chrom_stop_pos] = alt - elif nuc == ref: - count_ref += 1 - elif nuc == "N": - count_n += 1 - elif nuc == "lowQ": - count_lowq += 1 - else: - count_other += 1 - else: - count_indel += 1 - dcs_median = np.median(np.array(dcs_len)) - cvrg_dict[chrom_stop_pos] = (count_ref, count_alt, dcs_median) - - print("coverage at pos %s = %s, ref = %s, alt = %s, other bases = %s, N = %s, indel = %s, low quality = %s, median length of DCS = %s\n" % - (pileupcolumn.pos, count_ref + count_alt, count_ref, count_alt, count_other, count_n, - count_indel, count_lowq, dcs_median)) + print("coverage at pos %s = %s, ref = %s, alt = %s, other bases = %s, N = %s, indel = %s, low quality = %s, median length of DCS = %s\n" % + (pileupcolumn.pos, count_ref + count_alt, count_ref, count_alt, count_other, count_n, + count_indel, count_lowq, dcs_median)) + else: + print("indels are currently not evaluated") bam.close() with open(json_file, "w") as f: |
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| diff -r 3556001ff2db -r 3f1dbd2c59bf mut2read.xml --- a/mut2read.xml Wed Dec 04 16:21:17 2019 -0500 +++ b/mut2read.xml Tue Nov 10 12:55:29 2020 +0000 |
| [ |
| @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="mut2read" name="DCS mutations to tags/reads:" version="1.0.1" profile="19.01"> +<tool id="mut2read" name="DCS mutations to tags/reads:" version="2.0.0" profile="19.01"> <description>Extracts all tags that carry a mutation in the duplex consensus sequence (DCS)</description> <macros> <import>va_macros.xml</import> @@ -17,7 +17,7 @@ ]]> </command> <inputs> - <param name="file1" type="data" format="tabular" label="DCS Mutation File" optional="false" help="TABULAR file with DCS mutations. See Help section below for a detailed explanation."/> + <param name="file1" type="data" format="vcf" label="DCS Mutation File" optional="false" help="VCF file with DCS mutations. See Help section below for a detailed explanation."/> <param name="file2" type="data" format="bam" label="DCS BAM File" optional="false" help="BAM file with aligned DCS reads."/> <param name="file3" type="data" format="tabular" label="Aligned Families File" optional="false" help="TABULAR file with aligned families."/> </inputs> @@ -27,25 +27,25 @@ </outputs> <tests> <test> - <param name="file1" value="DCS_Mutations_test_data_VA.tabular"/> - <param name="file2" value="DCS_test_data_VA.bam"/> - <param name="file3" value="Aligned_Families_test_data_VA.tabular"/> - <output name="output_fastq" file="Interesting_Reads_test_data_VA.fastq" lines_diff="136"/> - <output name="output_json" file="tag_count_dict_test_data_VA.json" lines_diff="2"/> + <param name="file1" value="FreeBayes_test.vcf"/> + <param name="file2" value="DCS_test.bam"/> + <param name="file3" value="Aligned_Families_test.tabular"/> + <output name="output_fastq" file="Interesting_Reads_test.fastq"/> + <output name="output_json" file="tag_count_dict_test.json" lines_diff="2"/> </test> </tests> <help> <![CDATA[ **What it does** -Takes a tabular file with mutations, a BAM file of aligned DCS reads, and a +Takes a VCF file with mutations, a BAM file of aligned DCS reads, and a tabular file with aligned families as input and prints all tags of reads that carry a mutation to a user specified output file and creates a fastq file of reads of tags with a mutation. **Input** -**Dataset 1:** Tabular file with duplex consesus sequence (DCS) mutations as -generated by the **Variant Annotator** tool. +**Dataset 1:** VCF file with duplex consesus sequence (DCS) mutations. E.g. +generated by the `FreeBayes variant caller <https://arxiv.org/abs/1207.3907>`_. **Dataset 2:** BAM file of aligned DCS reads. This file can be obtained by the tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_. |
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| diff -r 3556001ff2db -r 3f1dbd2c59bf mut2sscs.py --- a/mut2sscs.py Wed Dec 04 16:21:17 2019 -0500 +++ b/mut2sscs.py Tue Nov 10 12:55:29 2020 +0000 |
| [ |
| b'@@ -11,7 +11,7 @@\n \n ======= ========== ================= ================================\n Version Date Author Description\n-0.2.1 2019-10-27 Gundula Povysil -\n+2.0.0 2020-10-30 Gundula Povysil -\n ======= ========== ================= ================================\n \n USAGE: python mut2sscs.py DCS_Mutations.tabular SSCS.bam SSCS_counts.json\n@@ -25,14 +25,14 @@\n import os\n import sys\n \n-import numpy as np\n import pysam\n+from cyvcf2 import VCF\n \n \n def make_argparser():\n- parser = argparse.ArgumentParser(description=\'Takes a tabular file with mutations and a BAM file as input and prints all tags of reads that carry the mutation to a user specified output file.\')\n+ parser = argparse.ArgumentParser(description=\'Takes a vcf file with mutations and a BAM file as input and prints all tags of reads that carry the mutation to a user specified output file.\')\n parser.add_argument(\'--mutFile\',\n- help=\'TABULAR file with DCS mutations.\')\n+ help=\'VCR file with DCS mutations.\')\n parser.add_argument(\'--bamFile\',\n help=\'BAM file with aligned SSCS reads.\')\n parser.add_argument(\'--outputJson\',\n@@ -54,74 +54,73 @@\n if os.path.isfile(file2) is False:\n sys.exit("Error: Could not find \'{}\'".format(file2))\n \n- # 1. read mut file\n- with open(file1, \'r\') as mut:\n- mut_array = np.genfromtxt(mut, skip_header=1, delimiter=\'\\t\', comments=\'#\', dtype=str)\n-\n- # 2 read SSCS bam file\n- # pysam.index(file2)\n+ # read SSCS bam file\n bam = pysam.AlignmentFile(file2, "rb")\n \n # get tags\n mut_pos_dict = {}\n ref_pos_dict = {}\n- if len(mut_array) == 13:\n- mut_array = mut_array.reshape((1, len(mut_array)))\n \n- for m in range(0, len(mut_array[:, 0])):\n- print(str(m + 1) + " of " + str(len(mut_array[:, 0])))\n- chrom = mut_array[m, 1]\n- stop_pos = mut_array[m, 2].astype(int)\n+ for variant in VCF(file1):\n+ chrom = variant.CHROM\n+ stop_pos = variant.start\n chrom_stop_pos = str(chrom) + "#" + str(stop_pos)\n- ref = mut_array[m, 9]\n- alt = mut_array[m, 10]\n+ ref = variant.REF\n+ alt = variant.ALT[0]\n \n- for pileupcolumn in bam.pileup(chrom, stop_pos - 2, stop_pos, max_depth=1000000000):\n- if pileupcolumn.reference_pos == stop_pos - 1:\n- count_alt = 0\n- count_ref = 0\n- count_indel = 0\n- print("unfiltered reads=", pileupcolumn.n, "filtered reads=", len(pileupcolumn.pileups),\n- "difference= ", len(pileupcolumn.pileups) - pileupcolumn.n)\n- for pileupread in pileupcolumn.pileups:\n- if not pileupread.is_del and not pileupread.is_refskip:\n- tag = pileupread.alignment.query_name\n- abba = tag[-2:]\n- # query position is None if is_del or is_refskip is set.\n- if pileupread.alignment.query_sequence[pileupread.query_position] == alt:\n- count_alt += 1\n- if chrom_stop_pos in mut_pos_dict:\n- if abba in mut_pos_dict[chrom_stop_pos]:\n- mut_pos_dict[chrom_stop_pos][abba] += 1\n+ if len(ref) == len(alt):\n+ for pileupcolumn in bam.pileup(chrom, stop_pos - 1, stop_pos + 1, max_depth=1000000000):\n+ if pileupcolumn.reference_pos == stop_pos:\n+ count_alt = 0\n+ count_ref = 0\n+ count_indel = 0\n+ print("unfiltered reads=", pileupcolumn.n, "filtered reads=", len(pileupcolumn.pileups),\n+ "difference= ", len(pileupcolumn.pileups) - pileupcolumn.n)\n+ for pileupread in pileupcolumn.pileups:\n+ if not pileupread.is_del and not pileupread.is_'..b' tag = pileupread.alignment.query_name\n+ abba = tag[-2:]\n+ # query position is None if is_del or is_refskip is set.\n+ if pileupread.alignment.query_sequence[pileupread.query_position] == alt:\n+ count_alt += 1\n+ if chrom_stop_pos in mut_pos_dict:\n+ if abba in mut_pos_dict[chrom_stop_pos]:\n+ mut_pos_dict[chrom_stop_pos][abba] += 1\n+ else:\n+ mut_pos_dict[chrom_stop_pos][abba] = 1\n else:\n+ mut_pos_dict[chrom_stop_pos] = {}\n mut_pos_dict[chrom_stop_pos][abba] = 1\n- else:\n- mut_pos_dict[chrom_stop_pos] = {}\n- mut_pos_dict[chrom_stop_pos][abba] = 1\n- elif pileupread.alignment.query_sequence[pileupread.query_position] == ref:\n- count_ref += 1\n- if chrom_stop_pos in ref_pos_dict:\n- if abba in ref_pos_dict[chrom_stop_pos]:\n- ref_pos_dict[chrom_stop_pos][abba] += 1\n+ if chrom_stop_pos not in ref_pos_dict:\n+ ref_pos_dict[chrom_stop_pos] = {}\n+ ref_pos_dict[chrom_stop_pos][abba] = 0\n+\n+ elif pileupread.alignment.query_sequence[pileupread.query_position] == ref:\n+ count_ref += 1\n+ if chrom_stop_pos in ref_pos_dict:\n+ if abba in ref_pos_dict[chrom_stop_pos]:\n+ ref_pos_dict[chrom_stop_pos][abba] += 1\n+ else:\n+ ref_pos_dict[chrom_stop_pos][abba] = 1\n else:\n+ ref_pos_dict[chrom_stop_pos] = {}\n ref_pos_dict[chrom_stop_pos][abba] = 1\n else:\n- ref_pos_dict[chrom_stop_pos] = {}\n- ref_pos_dict[chrom_stop_pos][abba] = 1\n- else:\n- count_indel += 1\n+ count_indel += 1\n \n- print("coverage at pos %s = %s, ref = %s, alt = %s, indel = %s,\\n" %\n- (pileupcolumn.pos, count_ref + count_alt, count_ref, count_alt, count_indel))\n+ print("coverage at pos %s = %s, ref = %s, alt = %s, indel = %s,\\n" %\n+ (pileupcolumn.pos, count_ref + count_alt, count_ref, count_alt, count_indel))\n \n- # if mutation is in DCS file but not in SSCS, then set counts to NA\n- if chrom_stop_pos not in mut_pos_dict.keys():\n- mut_pos_dict[chrom_stop_pos] = {}\n- mut_pos_dict[chrom_stop_pos]["ab"] = 0\n- mut_pos_dict[chrom_stop_pos]["ba"] = 0\n- ref_pos_dict[chrom_stop_pos] = {}\n- ref_pos_dict[chrom_stop_pos]["ab"] = 0\n- ref_pos_dict[chrom_stop_pos]["ba"] = 0\n+ # if mutation is in DCS file but not in SSCS, then set counts to NA\n+ if chrom_stop_pos not in mut_pos_dict.keys():\n+ mut_pos_dict[chrom_stop_pos] = {}\n+ mut_pos_dict[chrom_stop_pos]["ab"] = 0\n+ mut_pos_dict[chrom_stop_pos]["ba"] = 0\n+ ref_pos_dict[chrom_stop_pos] = {}\n+ ref_pos_dict[chrom_stop_pos]["ab"] = 0\n+ ref_pos_dict[chrom_stop_pos]["ba"] = 0\n+ else:\n+ print("indels are currently not evaluated")\n bam.close()\n \n # save counts\n' |
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| diff -r 3556001ff2db -r 3f1dbd2c59bf mut2sscs.xml --- a/mut2sscs.xml Wed Dec 04 16:21:17 2019 -0500 +++ b/mut2sscs.xml Tue Nov 10 12:55:29 2020 +0000 |
| [ |
| @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="mut2sscs" name="DCS mutations to SSCS stats:" version="1.0.1" profile="19.01"> +<tool id="mut2sscs" name="DCS mutations to SSCS stats:" version="2.0.0" profile="19.01"> <description>Extracts all tags from the single stranded consensus sequence (SSCS) bam file that carry a mutation at the same position a mutation is called in the duplex consensus sequence (DCS) and calculates their frequencies</description> <macros> <import>va_macros.xml</import> @@ -15,7 +15,7 @@ ]]> </command> <inputs> - <param name="file1" type="data" format="tabular" label="DCS Mutation File" optional="false" help="TABULAR file with DCS mutations. See Help section below for a detailed explanation."/> + <param name="file1" type="data" format="vcf" label="DCS Mutation File" optional="false" help="VCF file with DCS mutations. See Help section below for a detailed explanation."/> <param name="file2" type="data" format="bam" label="SSCS BAM File" optional="false" help="BAM file with aligned SSCS reads."/> </inputs> <outputs> @@ -23,31 +23,27 @@ </outputs> <tests> <test> - <param name="file1" value="DCS_Mutations_test_data_VA.tabular"/> - <param name="file2" value="SSCS_test_data_VA.bam"/> - <output name="output_json" file="SSCS_counts_test_data_VA.json" lines_diff="2"/> + <param name="file1" value="FreeBayes_test.vcf"/> + <param name="file2" value="SSCS_test.bam"/> + <output name="output_json" file="SSCS_counts_test.json" lines_diff="2"/> </test> </tests> <help> <![CDATA[ **What it does** -Takes a tabular file with DCS mutations and a BAM file of aligned SSCS reads +Takes a VCF file with DCS mutations and a BAM file of aligned SSCS reads as input and writes statistics about tags of reads that carry a mutation in the SSCS at the same position a mutation is called in the DCS to a user specified output file.. **Input** -**Dataset 1:** Tabular file with duplex consesus sequence (DCS) mutations as -generated by the **Variant Annotator** tool. +**Dataset 1:** VCF file with duplex consesus sequence (DCS) mutations. E.g. +generated by the `FreeBayes variant caller <https://arxiv.org/abs/1207.3907>`_. **Dataset 2:** BAM file of aligned single stranded consensus sequence (SSCS) reads. This file can be obtained by the tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_. -**Dataset 3:** Tabular file with reads as produced by the -**Du Novo: Align families** tool of the `Du Novo Analysis Pipeline -<https://doi.org/10.1186/s13059-016-1039-4>`_ - **Output** The output is a json file containing dictonaries with stats of tags that carry a mutation in the SSCS |
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| diff -r 3556001ff2db -r 3f1dbd2c59bf read2mut.py --- a/read2mut.py Wed Dec 04 16:21:17 2019 -0500 +++ b/read2mut.py Tue Nov 10 12:55:29 2020 +0000 |
| [ |
| b'@@ -10,13 +10,13 @@\n \n ======= ========== ================= ================================\n Version Date Author Description\n-0.2.1 2019-10-27 Gundula Povysil -\n+2.0.0 2020-10-30 Gundula Povysil -\n ======= ========== ================= ================================\n \n \n USAGE: python read2mut.py --mutFile DCS_Mutations.tabular --bamFile Interesting_Reads.trim.bam\n --inputJson tag_count_dict.json --sscsJson SSCS_counts.json\n- --outputFile mutant_reads_summary_short_trim.xlsx --thresh 10 --phred 20 --trim 10\n+ --outputFile mutant_reads_summary_short_trim.xlsx --thresh 10 --phred 20 --trim 10 --chimera_correction\n \n """\n \n@@ -32,12 +32,13 @@\n import numpy as np\n import pysam\n import xlsxwriter\n+from cyvcf2 import VCF\n \n \n def make_argparser():\n- parser = argparse.ArgumentParser(description=\'Takes a tabular file with mutations, a BAM file and JSON files as input and prints stats about variants to a user specified output file.\')\n+ parser = argparse.ArgumentParser(description=\'Takes a VCF file with mutations, a BAM file and JSON files as input and prints stats about variants to a user specified output file.\')\n parser.add_argument(\'--mutFile\',\n- help=\'TABULAR file with DCS mutations.\')\n+ help=\'VCF file with DCS mutations.\')\n parser.add_argument(\'--bamFile\',\n help=\'BAM file with aligned raw reads of selected tags (FASTQ created by mut2read.py - trimming with Trimmomatic - alignment with bwa).\')\n parser.add_argument(\'--inputJson\',\n@@ -52,6 +53,8 @@\n help=\'Integer threshold for Phred score. Only reads higher than this threshold are considered. Default 20.\')\n parser.add_argument(\'--trim\', type=int, default=10,\n help=\'Integer threshold for assigning mutations at start and end of reads to lower tier. Default 10.\')\n+ parser.add_argument(\'--chimera_correction\', action="store_true",\n+ help=\'Count chimeric variants and correct the variant frequencies\')\n return parser\n \n \n@@ -72,6 +75,7 @@\n thresh = args.thresh\n phred_score = args.phred\n trim = args.trim\n+ chimera_correction = args.chimera_correction\n \n if os.path.isfile(file1) is False:\n sys.exit("Error: Could not find \'{}\'".format(file1))\n@@ -86,95 +90,95 @@\n if trim < 0:\n sys.exit("Error: trim is \'{}\', but only non-negative integers allowed".format(thresh))\n \n- # 1. read mut file\n- with open(file1, \'r\') as mut:\n- mut_array = np.genfromtxt(mut, skip_header=1, delimiter=\'\\t\', comments=\'#\', dtype=str)\n-\n- # 2. load dicts\n+ # load dicts\n with open(json_file, "r") as f:\n (tag_dict, cvrg_dict) = json.load(f)\n \n with open(sscs_json, "r") as f:\n (mut_pos_dict, ref_pos_dict) = json.load(f)\n \n- # 3. read bam file\n- # pysam.index(file2)\n+ # read bam file\n bam = pysam.AlignmentFile(file2, "rb")\n \n- # 4. create mut_dict\n+ # create mut_dict\n mut_dict = {}\n mut_read_pos_dict = {}\n mut_read_dict = {}\n reads_dict = {}\n- if mut_array.shape == (13, ):\n- mut_array = mut_array.reshape((1, len(mut_array)))\n+ i = 0\n+ mut_array = []\n \n- for m in range(0, len(mut_array[:, 0])):\n- print(str(m + 1) + " of " + str(len(mut_array[:, 0])))\n- # for m in range(0, 5):\n- chrom = mut_array[m, 1]\n- stop_pos = mut_array[m, 2].astype(int)\n+ for variant in VCF(file1):\n+ chrom = variant.CHROM\n+ stop_pos = variant.start\n chrom_stop_pos = str(chrom) + "#" + str(stop_pos)\n- ref = mut_array[m, 9]\n- alt = mut_array[m, 10]\n- mut_dict[chrom_stop_pos] = {}\n- mut_read_pos_dict[chrom_stop_pos] = {}\n- reads_dict[chrom_stop_pos] = {}\n+ ref = variant.REF\n+ alt = variant.ALT[0]\n+\n+ if len(ref) == len(alt):\n+ '..b'ne, None, None,\n "269", "0", "0", "0", "0", "0", "0", "0", "0", None, None, None, None, "0",\n- "0", "0", "0", "1", "1", "5348", "5350", "", "")]]\n+ "0", "0", "0", "0", "0", "1", "1", "5348", "5350", "", "")]]\n \n- ws3.write(11, 0, "Description of tiers with examples")\n- ws3.write_row(12, 0, header_line)\n+ start_row = 15\n+ ws3.write(start_row, 0, "Description of tiers with examples")\n+ ws3.write_row(start_row + 1, 0, header_line)\n row = 0\n for i in range(len(description_tiers)):\n- ws3.write_row(13 + row + i + 1, 0, description_tiers[i])\n+ ws3.write_row(start_row + 2 + row + i + 1, 0, description_tiers[i])\n ex = examples_tiers[i]\n for k in range(len(ex)):\n- ws3.write_row(13 + row + i + k + 2, 0, ex[k])\n- ws3.conditional_format(\'L{}:M{}\'.format(13 + row + i + k + 2, 13 + row + i + k + 3), {\'type\': \'formula\', \'criteria\': \'=OR($B${}="1.1", $B${}="1.2")\'.format(13 + row + i + k + 2, 13 + row + i + k + 2), \'format\': format1, \'multi_range\': \'L{}:M{} T{}:U{} B{}\'.format(13 + row + i + k + 2, 13 + row + i + k + 3, 13 + row + i + k + 2, 13 + row + i + k + 3, 13 + row + i + k + 2, 13 + row + i + k + 3)})\n- ws3.conditional_format(\'L{}:M{}\'.format(13 + row + i + k + 2, 13 + row + i + k + 3),\n- {\'type\': \'formula\', \'criteria\': \'=OR($B${}="2.1",$B${}="2.2", $B${}="2.3", $B${}="2.4")\'.format(13 + row + i + k + 2, 13 + row + i + k + 2, 13 + row + i + k + 2, 13 + row + i + k + 2),\n+ ws3.write_row(start_row + 2 + row + i + k + 2, 0, ex[k])\n+ ws3.conditional_format(\'L{}:M{}\'.format(start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3), {\'type\': \'formula\', \'criteria\': \'=OR($B${}="1.1", $B${}="1.2")\'.format(start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 2), \'format\': format1, \'multi_range\': \'L{}:M{} T{}:U{} B{}\'.format(start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3, start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3, start_row + 2 + row + i + k + 2)})\n+ ws3.conditional_format(\'L{}:M{}\'.format(start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3),\n+ {\'type\': \'formula\', \'criteria\': \'=OR($B${}="2.1",$B${}="2.2", $B${}="2.3", $B${}="2.4")\'.format(start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 2),\n \'format\': format3,\n- \'multi_range\': \'L{}:M{} T{}:U{} B{}\'.format(13 + row + i + k + 2, 13 + row + i + k + 3, 13 + row + i + k + 2, 13 + row + i + k + 3, 13 + row + i + k + 2, 13 + row + i + k + 3)})\n- ws3.conditional_format(\'L{}:M{}\'.format(13 + row + i + k + 2, 13 + row + i + k + 3),\n+ \'multi_range\': \'L{}:M{} T{}:U{} B{}\'.format(start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3, start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3, start_row + 2 + row + i + k + 2)})\n+ ws3.conditional_format(\'L{}:M{}\'.format(start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3),\n {\'type\': \'formula\',\n- \'criteria\': \'=$B${}>="3"\'.format(13 + row + i + k + 2),\n+ \'criteria\': \'=$B${}>="3"\'.format(start_row + 2 + row + i + k + 2),\n \'format\': format2,\n- \'multi_range\': \'L{}:M{} T{}:U{} B{}\'.format(13 + row + i + k + 2, 13 + row + i + k + 3, 13 + row + i + k + 2, 13 + row + i + k + 3, 13 + row + i + k + 2, 13 + row + i + k + 3)})\n+ \'multi_range\': \'L{}:M{} T{}:U{} B{}\'.format(start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3, start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3, start_row + 2 + row + i + k + 2)})\n row += 3\n workbook.close()\n \n' |
| b |
| diff -r 3556001ff2db -r 3f1dbd2c59bf read2mut.xml --- a/read2mut.xml Wed Dec 04 16:21:17 2019 -0500 +++ b/read2mut.xml Tue Nov 10 12:55:29 2020 +0000 |
| [ |
| @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="read2mut" name="Call specific mutations in reads:" version="1.0.1" profile="19.01"> +<tool id="read2mut" name="Call specific mutations in reads:" version="2.0.0" profile="19.01"> <description>Looks for reads with mutation at known positions and calculates frequencies and stats.</description> <macros> <import>va_macros.xml</import> @@ -18,45 +18,48 @@ --thresh '$thresh' --phred '$phred' --trim '$trim' + $chimera_correction --outputFile '$output_xlsx' ]]> </command> <inputs> - <param name="file1" type="data" format="tabular" label="DCS Mutation File" optional="false" help="TABULAR file with DCS mutations. See Help section below for a detailed explanation."/> + <param name="file1" type="data" format="vcf" label="DCS Mutation File" optional="false" help="VCF file with DCS mutations. See Help section below for a detailed explanation."/> <param name="file2" type="data" format="bam" label="BAM File of raw reads" optional="false" help="BAM file with aligned raw reads of selected tags."/> <param name="file3" type="data" format="json" label="JSON File with DCS tag stats" optional="false" help="JSON file generated by DCS mutations to tags/reads"/> <param name="file4" type="data" format="json" label="JSON File with SSCS tag stats" optional="false" help="JSON file generated by DCS mutations to SSCS stats."/> <param name="thresh" type="integer" label="Tag count threshold" value="0" help="Integer threshold for displaying mutations. Only mutations occuring in DCS of less than thresh tags are displayed. Default of 0 displays all."/> <param name="phred" type="integer" label="Phred quality score threshold" min="0" max="41" value="20" help="Integer threshold for Phred quality score. Only reads higher than this threshold are considered. Default = 20."/> <param name="trim" type="integer" label="Trimming threshold" value="10" help="Integer threshold for assigning mutations at start and end of reads to lower tier. Default 10."/> + <param name="chimera_correction" type="boolean" label="Apply chimera correction?" truevalue="--chimera_correction" falsevalue="" checked="False" help="Count chimeric variants and correct the variant frequencies."/> </inputs> <outputs> <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX"/> </outputs> <tests> <test> - <param name="file1" value="DCS_Mutations_test_data_VA.tabular"/> - <param name="file2" value="Interesting_Reads_test_data_VA.trim.bam"/> - <param name="file3" value="tag_count_dict_test_data_VA.json"/> - <param name="file4" value="SSCS_counts_test_data_VA.json"/> + <param name="file1" value="FreeBayes_test.vcf"/> + <param name="file2" value="Interesting_Reads_test.trim.bam"/> + <param name="file3" value="tag_count_dict_test.json"/> + <param name="file4" value="SSCS_counts_test.json"/> <param name="thresh" value="0"/> <param name="phred" value="20"/> <param name="trim" value="10"/> - <output name="output_xlsx" file="mutant_reads_summary_short_trim_test_data_VA.xlsx" decompress="true" lines_diff="10"/> + <param name="chimera_correction" value="True"/> + <output name="output_xlsx" file="Variant_Analyzer_test.xlsx" decompress="true" lines_diff="2"/> </test> </tests> <help> <![CDATA[ **What it does** -Takes a tabular file with mutations, a BAM file of aligned raw reads, and JSON files +Takes a VCF file with mutations, a BAM file of aligned raw reads, and JSON files created by the tools **DCS mutations to tags/reads** and **DCS mutations to SSCS stats** as input and calculates frequencies and stats for DCS mutations based on information from the raw reads. **Input** -**Dataset 1:** Tabular file with duplex consesus sequence (DCS) mutations as -generated by the **Variant Annotator** tool. +**Dataset 1:** VCF file with duplex consesus sequence (DCS) mutations. E.g. +generated by the `FreeBayes variant caller <https://arxiv.org/abs/1207.3907>`_. **Dataset 2:** BAM file of aligned raw reads. This file can be obtained by the tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_. |
| b |
| diff -r 3556001ff2db -r 3f1dbd2c59bf test-data/Aligned_Families_test.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Aligned_Families_test.tabular Tue Nov 10 12:55:29 2020 +0000 |
| b |
| b'@@ -0,0 +1,41 @@\n+GATAACCTTGCTTCGTGATTAATC\tab\t1\tM01897:257:000000000-AYB6W:1:2112:28792:17250 2:N:0:1\tCTAGAGGGCCAGACCCTGGAGAGAATGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGTCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCACAGGGCCAGGAGTGAGGGCTCAAGAAGCGGGACGGCCGTAAGTCACAGGATTCCCGTCCGTCCTGGCAGCTTTGGCGTGTCCCGAGCCAGC\tGGGGGGGGGGGGGGFGFFGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGAFGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGFGG8<FED@FGEGGGGGGGGGGGGGGGGGGGGGGGGFEFGGGGGGGEEGGGGGGGGGCECE8EGGGEFFGGGGGGFGGGDEDD5EGGGGGFGGGDCFCFGFGFGCFAGGFDFFFEEGGFF3><:>>FD>FFC=4=:0<;DD>6461992<)892<AFBFFFFFF244:-1:1>:=0306(4)-.42((44(667(449?0,\n+GATAACCTTGCTTCGTGATTAATC\tba\t2\tM01897:257:000000000-AYB6W:1:1108:16316:3620 1:N:0:1\tCTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGTCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCACAGGGCCAGGAGGGAGGGCTCAAGAAGCGGGACGGCCGTAAGTCACAGGATTCCCGTCCGTCCTGGCAGCTTTGGCGTGTCCCGAGCCAGG\tGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGFGGGGGGGGGGFGGGGGGGGGGGFGGGGGGFCFGGGGFGGGGEGGFGGGGGGGFFGGGGGGGGGGGGGGGGBB?CFGGGGGGCCGGFGGGGGGGCFGECC79CEECGDDD99CFGGGGF4>>GG>BDE@BBFG5=B?AF98::A42<EF?;B::((7:?7???<)/:?91;1,6?F?29902(\n+GATAACCTTGCTTCGTGATTAATC\tba\t2\tM01897:257:000000000-AYB6W:1:1118:22651:3876 1:N:0:1\tCTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGTCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCACAGGGCCAGGAGTGAGGGCTCAAGAAGCGGGACGGCCGTAAGTCACAGGATTCCCGTCCGTCCTGGCAGCTTTGGCGTGTCCCGAGCCAGG\tGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGDGGGGEEGGGGGGGGGGGGGGGGGGGCEFDFGGGFGFGGEGEBFGG<FGFCFEFDFDF<DGGGGGGFGFGFGGGGGFGGGCE:FFBFGGGGDGGGGGGGGDD@FGGFC6AE7E1CGGFGCCFGGGGCEGFGGGCCFG9A*59@FGD><?9=CFF6>3BBDFFF392?G)-96<2<:<:44<232:B3:F>6??F0(34A248:>?1,(.404-,((4(\n+GATAACCTTGCTTCGTGATTAATC\tba\t2\tM01897:257:000000000-AYB6W:1:1118:5518:20674 1:N:0:1\tCTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACCCCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGTCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCACAGGGCCAGGAGTGAGGGCTCCAGAAGCGGGACGGCCGTAAGTCCCAGGATTCCCGTCCGTCCTGGCAGCTTTGGCGTGTCCCGAGCCAGC\tFGEF9FGGCCG@FGGGGGGCFCC@EGGG<FFGGFGGCGGGGGEG?FGGGGDGGGGGGGGFEFGGGGGGGGG7==F:F,=FEGGFFFFG<<F<=8FG>CAF9E8CFCEFFFFF,?F=F8FFD=,DFFE+@CGGGFF7D<FGGEFEGGFG2DCCFGECC*=CGEGGGGGGGGCCFFFGF7FFGFGGGGGGGFFG=E56C55CEGF3:F*9*./>FG***27)?::D)5557@>BFD@)/))).(().9<2((-29BF>F4(83,:12-)4)2,3??<<1:(7>((,\n+GATAACCTTGCTTCGTGATTAATC\tab\t2\tM01897:257:000000000-AYB6W:1:2112:28792:17250 1:N:0:1\tGATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTCTCCTTGCACAACGTCACCTTTGAGGACGCCGGGGAGTACACCTGCCTGGCGGGCAATTCTATTGGGTTTTCTCATCACTCTGCGTGGCTGGTGGTGCTGCCAGGTACCGGCTTCTGCTGCTGCTGCTGCTCCGCACTGTCTGGGGGACGCTGGCTCGGGACACG\tFGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGFGGGGGFFGGGGGGGGGGGGGGGGCFGGFFGGGCGGGGGGGGGCEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDFGGGGGGGGGGGGGGGGGGGGGGGGEGFGGFGFFGFGFGFFBEFGFFFF7F?FFB?DF>FDFFB:)9>FBFFF?F099E>;<?1:<?0>F0;BB1\n+GATAACCTTGCTTCGTGATTAATC\tba\t1\tM01897:257:000000000-AYB6W:1:1108:16316:3620 2:N:0:1\tGATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTCTCCTTGCACAACGTCACCTTTGAGGACGCCGGGGAGTACACCTGCCTGGCGGGCAATTCTATTGGGTTTTCTCATCACTCTGCGTGGCTGGTGGTGCTGCCAGGTACCGGCTTCTGCTGCTGCTGCTGCTCCGCACTGTCTGGGGGACGCTGGCGCGGGACACG\tGGGGGGGGGGGGGGGGGFGGGGGGGGGGGFGGGGGGGGGGGGGGDGGGGGGGGGGGFGGGGGGGGFGGGGGGGGGGGGDGCEEFGGGGGCGGGGGGGGGGGGGFGGGGGGGGFGGGGGGGGGGFGGGCGFFGGGGGGGGGGFFFFGGGGCEG==CECFFCDGGGGGGGGGGGGG597*<FGGFGDFC35>+*:=6FDFF4CFFF9B204>G?FE)5FAF?:7>FBB<A?FB(9?<AFFF<0?B?F4:BFF2>B69>;B))6<<?(,(46((4,42(7>926(82\n+GATAACCTTGCTTCGTGATTAATC\tba\t1\tM01897:257:000000000-AYB6'..b'4,7((-8)-8-71(--24641:B)47445270,(3124(.,(,:<>(. \n+CCTAGTCTTTGATTGGCCACTTTT\tab\t2\tM01897:257:000000000-AYB6W:1:1106:12553:14962 1:N:0:1\tCTAGACTCACTGGCGTTACTGACTGCGAGACCCTCCAGACAAGGCGCGTGCTGAGGTTCTGAGCCCCCTTCCGCTCCCAGTGGTGCCTGCGGCTCTGGGCCAGGGGCATCCATGGGAGCCCCGTGGGGGGGGGGG--CCAGGCAGGGCCCCAAGCCCCTTGTCT-TGCAGCCGGGGGGGGGGCGGTGGGAGCCTAACAAGCGGGGCGGGGGGTTGGAGGCCTCCCCAAGTTCGGGGGTGGCTTCTTCCTGTTCATCCTTGGTGTGGGGGCTGTGACGCCTTTGCGGC\tGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG* ?8*;*;**:*;***2***2A***00+< C++0++;***:**:*****://:**;**0++*++2*/:E/*1**)))/)1)+*1**))9))**)/**)03>))8D)(8().5<*)-7))1)67)6/.8118((4(-,.()-(()(-)).(,-\n+CCTAGTCTTTGATTGGCCACTTTT\tab\t2\tM01897:257:000000000-AYB6W:1:1106:15615:18803 1:N:0:1\tCTAGACTCACTGGCGTTACTGACTGCGAGACCCTCCAGACAAGGCGCGTGCTGAGGTTCTGAGCCCCCTTCCGCTCCCAGTGGTGCCTGCGGCTCTGGGCCAGGGGCATCCATGGGAGCCCCGTGGGGGGGGGGA--CCAGGCCAGGCCTCAACGCCCATGTCTTTGCAGCCGAGGAGGAGCTGGTGGAGGCTGACGAGGCGGGCAGTGTGTATGCAGGCATCCTCAGCTACGGGGTGGGCTTCTTCCTGTTCATCCTGGTGGTGGCGGCTGTGACGCTCTGCC-GC\tGGGGGFGGGGFGGGGGGGGGFGGGGGGGGGGEGGGGGGGGGDEFGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGCFGGGGGGGCFGEGFGEEGGGGGGGDGGDGGCFGGGGGGGDGGGGGGFGGGGGGGGGGG GDGGGGGGGFGGGGFGGGGGGGGGFGG9FFGGGGGGGGGCEGECGGCFCEEGGGGGGGGGGGCGGCEC3*:C>DG=FC<?CGGFFGFFFGFFGFFFFFG:BDFFF<:AFFFFFFFF4<4?BAFB:<BB??09>B0?B><:D243847 10\n+CCTAGTCTTTGATTGGCCACTTTT\tab\t2\tM01897:257:000000000-AYB6W:1:1110:11692:17499 1:N:0:1\tCTAGACTCACTGGCGTTACTGACTGCGAGACCCTCCAGACAAGGCGCGTGCTGAGGTTCTGAGCCCCCTTCCGCTCCCAGTGGTGCCTGCGGCTCTGGGCCAGGGGCATCCATGGGAGCCCCGTGGGGGGGGGGGGGCCAGGCCAGGCCCCAACGCCCATGTCTTTGCAGCCGAGGGGGAGCTGGTTGGGGCTGACGAGGCGGGCAGTGGGTATGCAGGCATCCTCAGCTACGGGGTGGGCTTCTTCCTGTTCATCCTGGGGGTGGCGGCTTGTACCCTCTTCC---\tGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG8>5*;:8C8E@;?*:;88*2CE*8*++<C99+9+@C**88*:C*:?6<C*+1*:858C*;7/9E*1CGCCC0*)1)*+<C7C.5766<69=<))9*05>3/4;<31<2)9:4=).0))/69?<((213(7:960(,1.-))))(()-) \n+GATAAGCCAACTGCCATCTAGAAT\tab\t1\tM01897:257:000000000-AYB6W:1:1105:25798:19415 2:N:0:1\tCTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGTCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCACAGGGCCAGGAGTGAGGGCTCAAGAAGCGGGACGGCCGTACGTCACAGGATTCCCGTCCGTCCTGGCAGCTTTGGCGTTTCCCGAGCCAGC\tGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGFGGGFGGGGGGGGGGGGGGEFCFFGGDEGG8EGGGGFGGGGEGFEGFFG<EDGGGGGGGGGCC7FGGGGGGGFGG=>FFCDBF)7:>7FF:EF?<?FEE:@F@?6??F6>B01>BF;FFF*4(,2:24?FBBF>?F?FFBF0;B2:0(:??FF7:BF?03:2<BBFBFB?0\n+GATAAGCCAACTGCCATCTAGAAT\tba\t2\tM01897:257:000000000-AYB6W:1:2104:15100:19675 1:N:0:1\tCTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGGCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCACAGGGCCAGGAGTGAGGGCTCAAGAAGCGGGACGGCCGTAAGTCACAGGATTCCCGTCCGTCCTGGCAGCTTTCGCGTGTCCCGAGCCAGC\tGGFGFGGDGGGGGGCGGGD@EFGGFFGEGGGGGGGFECDEDFFGGGFGGGGFGDEGDGGEGGGGGG:FGGG@CFECFGGGGGFFGGGGGGF<CGGEGGGEFGGGEE7FGFF,=B=DBBFFDDFFFGGGGGGGEGGG:><FEGCF:FGEFGGFFFGGGDGGFEGDFGGGFGGGFFGGGCGGGEGFGGGGFFCFFEDG57CGGCFFC6C*CEGG6:CGGG:6<C>>CEFDGB7B5/<<:9<>>><F279?FG<>>>:>:D(47:6<26)402346>2<>(-49??0\n+GATAAGCCAACTGCCATCTAGAAT\tab\t2\tM01897:257:000000000-AYB6W:1:1105:25798:19415 1:N:0:1\tGATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTCTCCTTGCACAACGTCACCTTTGAGGACGCCGGGGAGTACACCTGCCTGGCGGGCAATTCTATTGGGTTTTCTCATCACTCTGCGTGGCTGGTGGTGCTGCCAGGTACCGGCTTCTGCTGCTGCTGCTGCTCCGCACTGTCTGGGGGACGCTGGCTCGGGACACG\tGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFFFFGGFFGDB9FFGFFFF0F?:?FFFFFFFFFFFFBF@FFBA?B9;9B9>BB>FFF>FF>><?4\n' |
| b |
| diff -r 3556001ff2db -r 3f1dbd2c59bf test-data/Aligned_Families_test_data_VA.tabular --- a/test-data/Aligned_Families_test_data_VA.tabular Wed Dec 04 16:21:17 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,41 +0,0 @@\n-GATAACCTTGCTTCGTGATTAATC\tab\t1\tM01897:257:000000000-AYB6W:1:2112:28792:17250 2:N:0:1\tCTAGAGGGCCAGACCCTGGAGAGAATGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGTCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCACAGGGCCAGGAGTGAGGGCTCAAGAAGCGGGACGGCCGTAAGTCACAGGATTCCCGTCCGTCCTGGCAGCTTTGGCGTGTCCCGAGCCAGC\tGGGGGGGGGGGGGGFGFFGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGAFGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGFGG8<FED@FGEGGGGGGGGGGGGGGGGGGGGGGGGFEFGGGGGGGEEGGGGGGGGGCECE8EGGGEFFGGGGGGFGGGDEDD5EGGGGGFGGGDCFCFGFGFGCFAGGFDFFFEEGGFF3><:>>FD>FFC=4=:0<;DD>6461992<)892<AFBFFFFFF244:-1:1>:=0306(4)-.42((44(667(449?0,\n-GATAACCTTGCTTCGTGATTAATC\tba\t2\tM01897:257:000000000-AYB6W:1:1108:16316:3620 1:N:0:1\tCTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGTCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCACAGGGCCAGGAGGGAGGGCTCAAGAAGCGGGACGGCCGTAAGTCACAGGATTCCCGTCCGTCCTGGCAGCTTTGGCGTGTCCCGAGCCAGG\tGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGFGGGGGGGGGGFGGGGGGGGGGGFGGGGGGFCFGGGGFGGGGEGGFGGGGGGGFFGGGGGGGGGGGGGGGGBB?CFGGGGGGCCGGFGGGGGGGCFGECC79CEECGDDD99CFGGGGF4>>GG>BDE@BBFG5=B?AF98::A42<EF?;B::((7:?7???<)/:?91;1,6?F?29902(\n-GATAACCTTGCTTCGTGATTAATC\tba\t2\tM01897:257:000000000-AYB6W:1:1118:22651:3876 1:N:0:1\tCTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGTCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCACAGGGCCAGGAGTGAGGGCTCAAGAAGCGGGACGGCCGTAAGTCACAGGATTCCCGTCCGTCCTGGCAGCTTTGGCGTGTCCCGAGCCAGG\tGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGDGGGGEEGGGGGGGGGGGGGGGGGGGCEFDFGGGFGFGGEGEBFGG<FGFCFEFDFDF<DGGGGGGFGFGFGGGGGFGGGCE:FFBFGGGGDGGGGGGGGDD@FGGFC6AE7E1CGGFGCCFGGGGCEGFGGGCCFG9A*59@FGD><?9=CFF6>3BBDFFF392?G)-96<2<:<:44<232:B3:F>6??F0(34A248:>?1,(.404-,((4(\n-GATAACCTTGCTTCGTGATTAATC\tba\t2\tM01897:257:000000000-AYB6W:1:1118:5518:20674 1:N:0:1\tCTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACCCCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGTCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCACAGGGCCAGGAGTGAGGGCTCCAGAAGCGGGACGGCCGTAAGTCCCAGGATTCCCGTCCGTCCTGGCAGCTTTGGCGTGTCCCGAGCCAGC\tFGEF9FGGCCG@FGGGGGGCFCC@EGGG<FFGGFGGCGGGGGEG?FGGGGDGGGGGGGGFEFGGGGGGGGG7==F:F,=FEGGFFFFG<<F<=8FG>CAF9E8CFCEFFFFF,?F=F8FFD=,DFFE+@CGGGFF7D<FGGEFEGGFG2DCCFGECC*=CGEGGGGGGGGCCFFFGF7FFGFGGGGGGGFFG=E56C55CEGF3:F*9*./>FG***27)?::D)5557@>BFD@)/))).(().9<2((-29BF>F4(83,:12-)4)2,3??<<1:(7>((,\n-GATAACCTTGCTTCGTGATTAATC\tab\t2\tM01897:257:000000000-AYB6W:1:2112:28792:17250 1:N:0:1\tGATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTCTCCTTGCACAACGTCACCTTTGAGGACGCCGGGGAGTACACCTGCCTGGCGGGCAATTCTATTGGGTTTTCTCATCACTCTGCGTGGCTGGTGGTGCTGCCAGGTACCGGCTTCTGCTGCTGCTGCTGCTCCGCACTGTCTGGGGGACGCTGGCTCGGGACACG\tFGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGFGGGGGFFGGGGGGGGGGGGGGGGCFGGFFGGGCGGGGGGGGGCEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDFGGGGGGGGGGGGGGGGGGGGGGGGEGFGGFGFFGFGFGFFBEFGFFFF7F?FFB?DF>FDFFB:)9>FBFFF?F099E>;<?1:<?0>F0;BB1\n-GATAACCTTGCTTCGTGATTAATC\tba\t1\tM01897:257:000000000-AYB6W:1:1108:16316:3620 2:N:0:1\tGATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTCTCCTTGCACAACGTCACCTTTGAGGACGCCGGGGAGTACACCTGCCTGGCGGGCAATTCTATTGGGTTTTCTCATCACTCTGCGTGGCTGGTGGTGCTGCCAGGTACCGGCTTCTGCTGCTGCTGCTGCTCCGCACTGTCTGGGGGACGCTGGCGCGGGACACG\tGGGGGGGGGGGGGGGGGFGGGGGGGGGGGFGGGGGGGGGGGGGGDGGGGGGGGGGGFGGGGGGGGFGGGGGGGGGGGGDGCEEFGGGGGCGGGGGGGGGGGGGFGGGGGGGGFGGGGGGGGGGFGGGCGFFGGGGGGGGGGFFFFGGGGCEG==CECFFCDGGGGGGGGGGGGG597*<FGGFGDFC35>+*:=6FDFF4CFFF9B204>G?FE)5FAF?:7>FBB<A?FB(9?<AFFF<0?B?F4:BFF2>B69>;B))6<<?(,(46((4,42(7>926(82\n-GATAACCTTGCTTCGTGATTAATC\tba\t1\tM01897:257:000000000-AYB6'..b'4,7((-8)-8-71(--24641:B)47445270,(3124(.,(,:<>(. \n-CCTAGTCTTTGATTGGCCACTTTT\tab\t2\tM01897:257:000000000-AYB6W:1:1106:12553:14962 1:N:0:1\tCTAGACTCACTGGCGTTACTGACTGCGAGACCCTCCAGACAAGGCGCGTGCTGAGGTTCTGAGCCCCCTTCCGCTCCCAGTGGTGCCTGCGGCTCTGGGCCAGGGGCATCCATGGGAGCCCCGTGGGGGGGGGGG--CCAGGCAGGGCCCCAAGCCCCTTGTCT-TGCAGCCGGGGGGGGGGCGGTGGGAGCCTAACAAGCGGGGCGGGGGGTTGGAGGCCTCCCCAAGTTCGGGGGTGGCTTCTTCCTGTTCATCCTTGGTGTGGGGGCTGTGACGCCTTTGCGGC\tGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG* ?8*;*;**:*;***2***2A***00+< C++0++;***:**:*****://:**;**0++*++2*/:E/*1**)))/)1)+*1**))9))**)/**)03>))8D)(8().5<*)-7))1)67)6/.8118((4(-,.()-(()(-)).(,-\n-CCTAGTCTTTGATTGGCCACTTTT\tab\t2\tM01897:257:000000000-AYB6W:1:1106:15615:18803 1:N:0:1\tCTAGACTCACTGGCGTTACTGACTGCGAGACCCTCCAGACAAGGCGCGTGCTGAGGTTCTGAGCCCCCTTCCGCTCCCAGTGGTGCCTGCGGCTCTGGGCCAGGGGCATCCATGGGAGCCCCGTGGGGGGGGGGA--CCAGGCCAGGCCTCAACGCCCATGTCTTTGCAGCCGAGGAGGAGCTGGTGGAGGCTGACGAGGCGGGCAGTGTGTATGCAGGCATCCTCAGCTACGGGGTGGGCTTCTTCCTGTTCATCCTGGTGGTGGCGGCTGTGACGCTCTGCC-GC\tGGGGGFGGGGFGGGGGGGGGFGGGGGGGGGGEGGGGGGGGGDEFGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGCFGGGGGGGCFGEGFGEEGGGGGGGDGGDGGCFGGGGGGGDGGGGGGFGGGGGGGGGGG GDGGGGGGGFGGGGFGGGGGGGGGFGG9FFGGGGGGGGGCEGECGGCFCEEGGGGGGGGGGGCGGCEC3*:C>DG=FC<?CGGFFGFFFGFFGFFFFFG:BDFFF<:AFFFFFFFF4<4?BAFB:<BB??09>B0?B><:D243847 10\n-CCTAGTCTTTGATTGGCCACTTTT\tab\t2\tM01897:257:000000000-AYB6W:1:1110:11692:17499 1:N:0:1\tCTAGACTCACTGGCGTTACTGACTGCGAGACCCTCCAGACAAGGCGCGTGCTGAGGTTCTGAGCCCCCTTCCGCTCCCAGTGGTGCCTGCGGCTCTGGGCCAGGGGCATCCATGGGAGCCCCGTGGGGGGGGGGGGGCCAGGCCAGGCCCCAACGCCCATGTCTTTGCAGCCGAGGGGGAGCTGGTTGGGGCTGACGAGGCGGGCAGTGGGTATGCAGGCATCCTCAGCTACGGGGTGGGCTTCTTCCTGTTCATCCTGGGGGTGGCGGCTTGTACCCTCTTCC---\tGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG8>5*;:8C8E@;?*:;88*2CE*8*++<C99+9+@C**88*:C*:?6<C*+1*:858C*;7/9E*1CGCCC0*)1)*+<C7C.5766<69=<))9*05>3/4;<31<2)9:4=).0))/69?<((213(7:960(,1.-))))(()-) \n-GATAAGCCAACTGCCATCTAGAAT\tab\t1\tM01897:257:000000000-AYB6W:1:1105:25798:19415 2:N:0:1\tCTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGTCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCACAGGGCCAGGAGTGAGGGCTCAAGAAGCGGGACGGCCGTACGTCACAGGATTCCCGTCCGTCCTGGCAGCTTTGGCGTTTCCCGAGCCAGC\tGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGFGGGFGGGGGGGGGGGGGGEFCFFGGDEGG8EGGGGFGGGGEGFEGFFG<EDGGGGGGGGGCC7FGGGGGGGFGG=>FFCDBF)7:>7FF:EF?<?FEE:@F@?6??F6>B01>BF;FFF*4(,2:24?FBBF>?F?FFBF0;B2:0(:??FF7:BF?03:2<BBFBFB?0\n-GATAAGCCAACTGCCATCTAGAAT\tba\t2\tM01897:257:000000000-AYB6W:1:2104:15100:19675 1:N:0:1\tCTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGGCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCACAGGGCCAGGAGTGAGGGCTCAAGAAGCGGGACGGCCGTAAGTCACAGGATTCCCGTCCGTCCTGGCAGCTTTCGCGTGTCCCGAGCCAGC\tGGFGFGGDGGGGGGCGGGD@EFGGFFGEGGGGGGGFECDEDFFGGGFGGGGFGDEGDGGEGGGGGG:FGGG@CFECFGGGGGFFGGGGGGF<CGGEGGGEFGGGEE7FGFF,=B=DBBFFDDFFFGGGGGGGEGGG:><FEGCF:FGEFGGFFFGGGDGGFEGDFGGGFGGGFFGGGCGGGEGFGGGGFFCFFEDG57CGGCFFC6C*CEGG6:CGGG:6<C>>CEFDGB7B5/<<:9<>>><F279?FG<>>>:>:D(47:6<26)402346>2<>(-49??0\n-GATAAGCCAACTGCCATCTAGAAT\tab\t2\tM01897:257:000000000-AYB6W:1:1105:25798:19415 1:N:0:1\tGATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTCTCCTTGCACAACGTCACCTTTGAGGACGCCGGGGAGTACACCTGCCTGGCGGGCAATTCTATTGGGTTTTCTCATCACTCTGCGTGGCTGGTGGTGCTGCCAGGTACCGGCTTCTGCTGCTGCTGCTGCTCCGCACTGTCTGGGGGACGCTGGCTCGGGACACG\tGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFFFFGGFFGDB9FFGFFFF0F?:?FFFFFFFFFFFFBF@FFBA?B9;9B9>BB>FFF>FF>><?4\n' |
| b |
| diff -r 3556001ff2db -r 3f1dbd2c59bf test-data/DCS_Mutations_test_data_VA.tabular --- a/test-data/DCS_Mutations_test_data_VA.tabular Wed Dec 04 16:21:17 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,5 +0,0 @@ -#SAMPLE CHR POS A C G T CVRG ALLELES MAJOR MINOR MAF BIAS -__NONE__ ACH_TDII_5regions 505 1 2208 0 0 2209 1 C A 0.00045 1.09465 -__NONE__ ACH_TDII_5regions 571 0 2817 0 1 2818 1 C T 0.00035 1.04139 -__NONE__ ACH_TDII_5regions 958 0 1 0 14667 14668 1 T C 7e-05 1.03624 - |
| b |
| diff -r 3556001ff2db -r 3f1dbd2c59bf test-data/DCS_test.bam |
| b |
| Binary file test-data/DCS_test.bam has changed |
| b |
| diff -r 3556001ff2db -r 3f1dbd2c59bf test-data/DCS_test.bam.bai |
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| Binary file test-data/DCS_test.bam.bai has changed |
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| diff -r 3556001ff2db -r 3f1dbd2c59bf test-data/DCS_test_data_VA.bam |
| b |
| Binary file test-data/DCS_test_data_VA.bam has changed |
| b |
| diff -r 3556001ff2db -r 3f1dbd2c59bf test-data/DCS_test_data_VA.bam.bai |
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| Binary file test-data/DCS_test_data_VA.bam.bai has changed |
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| diff -r 3556001ff2db -r 3f1dbd2c59bf test-data/FreeBayes_test.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/FreeBayes_test.vcf Tue Nov 10 12:55:29 2020 +0000 |
| b |
| b'@@ -0,0 +1,65 @@\n+##fileformat=VCFv4.2\n+##fileDate=20201027\n+##source=freeBayes v1.3.1-dirty\n+##reference=localref.fa\n+##contig=<ID=ACH_TDII_5regions,length=3171>\n+##phasing=none\n+##commandline="freebayes --region ACH_TDII_5regions:0..3171 --bam b_0.bam --fasta-reference localref.fa --vcf ./vcf_output/part_ACH_TDII_5regions:0..3171.vcf --min-coverage 1 --skip-coverage 0 --limit-coverage 0 -O -m 1 -q 0 -R 0 -Y 0 -e 1000 -F 0.0 -C 1 -G 1 --min-alternate-qsum 0"\n+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">\n+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">\n+##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">\n+##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">\n+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">\n+##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">\n+##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">\n+##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">\n+##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">\n+##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">\n+##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">\n+##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">\n+##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations">\n+##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations">\n+##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">\n+##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">\n+##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand">\n+##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand">\n+##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding\'s inequality">\n+##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding\'s inequality">\n+##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">\n+##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding\'s inequality">\n+##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">\n+##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding\'s inequality">\n+##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviatio'..b'ired to reach convergence or bailout.">\n+##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">\n+##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that \'=\' is replaced by \'M\' to ease VCF parsing. Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.">\n+##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position.">\n+##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.">\n+##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">\n+##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles">\n+##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles">\n+##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments">\n+##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments">\n+##INFO=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">\n+##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record.">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">\n+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">\n+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Number of observation for each allele">\n+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">\n+##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">\n+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">\n+##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">\n+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">\n+##INFO=<ID=Split primitives,Number=0,Type=Flag,Description="The allele was parsed using vcfallelicprimitives.">\n+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tunknown\n+ACH_TDII_5regions\t505\t.\tC\tA\t21.9913\t.\tAB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=5.18177;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=5.05096;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=93;QR=93;RO=1;RPL=0;RPP=5.18177;RPPR=5.18177;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0/1:2:1,1:1:93:1:93:-5.39772,0,-5.39772\n+ACH_TDII_5regions\t571\t.\tC\tT\t21.9913\t.\tAB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=5.18177;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=5.05096;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=93;QR=93;RO=1;RPL=1;RPP=5.18177;RPPR=5.18177;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0/1:2:1,1:1:93:1:93:-5.39772,0,-5.39772\n+ACH_TDII_5regions\t958\t.\tT\tC\t50.9778\t.\tAB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPB=1;DPRA=0;EPP=5.18177;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=5.99146;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=93;QR=0;RO=0;RPL=0;RPP=5.18177;RPPR=0;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t1/1:1:0,1:0:0:1:93:-5.99978,-0.30103,0\n' |
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| diff -r 3556001ff2db -r 3f1dbd2c59bf test-data/Interesting_Reads_test.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Interesting_Reads_test.fastq Tue Nov 10 12:55:29 2020 +0000 |
| b |
| b'@@ -0,0 +1,124 @@\n+@GATAACCTTGCTTCGTGATTAATC.ab.1\n+CTAGAGGGCCAGACCCTGGAGAGAATGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGTCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCACAGGGCCAGGAGTGAGGGCTCAAGAAGCGGGACGGCCGTAAGTCACAGGATTCCCGTCCGTCCTGGCAGCTTTGGCGTGTCCCGAGCCAGC\n++\n+GGGGGGGGGGGGGGFGFFGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGAFGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGFGG8<FED@FGEGGGGGGGGGGGGGGGGGGGGGGGGFEFGGGGGGGEEGGGGGGGGGCECE8EGGGEFFGGGGGGFGGGDEDD5EGGGGGFGGGDCFCFGFGFGCFAGGFDFFFEEGGFF3><:>>FD>FFC=4=:0<;DD>6461992<)892<AFBFFFFFF244:-1:1>:=0306(4)-.42((44(667(449?0,\n+@GATAACCTTGCTTCGTGATTAATC.ba.2\n+CTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGTCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCACAGGGCCAGGAGGGAGGGCTCAAGAAGCGGGACGGCCGTAAGTCACAGGATTCCCGTCCGTCCTGGCAGCTTTGGCGTGTCCCGAGCCAGG\n++\n+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGFGGGGGGGGGGFGGGGGGGGGGGFGGGGGGFCFGGGGFGGGGEGGFGGGGGGGFFGGGGGGGGGGGGGGGGBB?CFGGGGGGCCGGFGGGGGGGCFGECC79CEECGDDD99CFGGGGF4>>GG>BDE@BBFG5=B?AF98::A42<EF?;B::((7:?7???<)/:?91;1,6?F?29902(\n+@GATAACCTTGCTTCGTGATTAATC.ba.2\n+CTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGTCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCACAGGGCCAGGAGTGAGGGCTCAAGAAGCGGGACGGCCGTAAGTCACAGGATTCCCGTCCGTCCTGGCAGCTTTGGCGTGTCCCGAGCCAGG\n++\n+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGDGGGGEEGGGGGGGGGGGGGGGGGGGCEFDFGGGFGFGGEGEBFGG<FGFCFEFDFDF<DGGGGGGFGFGFGGGGGFGGGCE:FFBFGGGGDGGGGGGGGDD@FGGFC6AE7E1CGGFGCCFGGGGCEGFGGGCCFG9A*59@FGD><?9=CFF6>3BBDFFF392?G)-96<2<:<:44<232:B3:F>6??F0(34A248:>?1,(.404-,((4(\n+@GATAACCTTGCTTCGTGATTAATC.ba.2\n+CTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACCCCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGTCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCACAGGGCCAGGAGTGAGGGCTCCAGAAGCGGGACGGCCGTAAGTCCCAGGATTCCCGTCCGTCCTGGCAGCTTTGGCGTGTCCCGAGCCAGC\n++\n+FGEF9FGGCCG@FGGGGGGCFCC@EGGG<FFGGFGGCGGGGGEG?FGGGGDGGGGGGGGFEFGGGGGGGGG7==F:F,=FEGGFFFFG<<F<=8FG>CAF9E8CFCEFFFFF,?F=F8FFD=,DFFE+@CGGGFF7D<FGGEFEGGFG2DCCFGECC*=CGEGGGGGGGGCCFFFGF7FFGFGGGGGGGFFG=E56C55CEGF3:F*9*./>FG***27)?::D)5557@>BFD@)/))).(().9<2((-29BF>F4(83,:12-)4)2,3??<<1:(7>((,\n+@GATAACCTTGCTTCGTGATTAATC.ab.2\n+GATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTCTCCTTGCACAACGTCACCTTTGAGGACGCCGGGGAGTACACCTGCCTGGCGGGCAATTCTATTGGGTTTTCTCATCACTCTGCGTGGCTGGTGGTGCTGCCAGGTACCGGCTTCTGCTGCTGCTGCTGCTCCGCACTGTCTGGGGGACGCTGGCTCGGGACACG\n++\n+FGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGFGGGGGFFGGGGGGGGGGGGGGGGCFGGFFGGGCGGGGGGGGGCEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDFGGGGGGGGGGGGGGGGGGGGGGGGEGFGGFGFFGFGFGFFBEFGFFFF7F?FFB?DF>FDFFB:)9>FBFFF?F099E>;<?1:<?0>F0;BB1\n+@GATAACCTTGCTTCGTGATTAATC.ba.1\n+GATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTCTCCTTGCACAACGTCACCTTTGAGGACGCCGGGGAGTACACCTGCCTGGCGGGCAATTCTATTGGGTTTTCTCATCACTCTGCGTGGCTGGTGGTGCTGCCAGGTACCGGCTTCTGCTGCTGCTGCTGCTCCGCACTGTCTGGGGGACGCTGGCGCGGGACACG\n++\n+GGGGGGGGGGGGGGGGGFGGGGGGGGGGGFGGGGGGGGGGGGGGDGGGGGGGGGGGFGGGGGGGGFGGGGGGGGGGGGDGCEEFGGGGGCGGGGGGGGGGGGGFGGGGGGGGFGGGGGGGGGGFGGGCGFFGGGGGGGGGGFFFFGGGGCEG==CECFFCDGGGGGGGGGGGGG597*<FGGFGDFC35>+*:=6FDFF4CFFF9B204>G?FE)5FAF?:7>FBB<A?FB(9?<AFFF<0?B?F4:BFF2>B69>;B))6<<?(,(46((4,42(7>926(82\n+@GATAACCTTGCTTCGTGATTAATC.ba.1\n+GATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTCTCCTTGCACAACGTCACCTTTGAGGACGCCGGGGAGTACACCTGCCTGGCGGGCAATTCTATTGGGTTTTCTCATCACTCTGCGTGGCTGGTGGTTCTGCCAGGTACCGGCTTCTGCTGCTGCTGCTGCTCCGCACTGTCTGGGGGACGCTGGCCCGGGACACG\n++\n+FDCCF9FFDFGGGGGGG'..b'CAGGCTCCCTACGCTACGGGGTGGGCTTTTTCCGTTTCATCTTGGTGTTGCCGGCTGGGACGCCTTGCGCC\n++\n+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG7FGGGGGGGGGGGC<FGGGDGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGDEC8C>C5*:/C:*:<+2/>C:*:*+*<>?+*+0<5:/>E5<35***<6293*935=DC)))1707C5)(1*))())()*06)(((0,(*(,(,(-4(9),4D6(4((5)4*(,).2))-).5)5:228))-1(-(((((-((,()5(-(\n+@CCTCCCGGCAGTGCGAAAATGTCA.ba.2\n+CTAGACTCACTGGCGTTACTGACTGCGAGACCCTCCAGACAAGGCGCGTGCTGAGGTTCTGAGCCCCCTTCCGCTCCCAGTGGTGCCTGCGGCTCTGGGCCAGGGGCATCCATGGGAGCCCCGTGGGGGGGGGGCCAGGCCAGGCCTCAACGCCCATGTCTTTGCAGCCGAGGAGGAGCTGGTGGAGGCTGACGACGCGGGCAGTGTGTATGCAGTCATCCTCAGCTACGGGCTGGGCTTCTTCCTGTTTATCCTGGTGGTGGCGGCTGTGTCGCTCTGCCGTC\n++\n+CFGGAFCFCFGGGFDGDDDGGDGGGG;F:BFGEGFGGGGFF<FFDECG@CFDGGF@FECFAEGFGGGGGAFFEGGGEGF<?E@FFGFEFGEGG+BEF=<FGGCFCFGGGGGGGG8FDFGGDF@FFGGGEEG*88:C88AFEC>8A:@;EFG8>:EEGE0<CCF+<E:CE/C8C*8C*;;C:0*;=EFEDG*/0*7*:7*18*27:CFGD?>>7+CGG>?F:?4*7?FG6).-))7)/<BF0)6.)/--/)67.:F209304(((493(,:5-)(2;:<2).4((\n+@CCTCCCGGCAGTGCGAAAATGTCA.ba.2\n+CTAGACTCACTGGCGTTACTGACTGCGAGACCCTCCAGACAAGGCGCGTGCTGAGGTTCTGAGCCCCCTTCCGCTCCCAGTGGTGCCTGCGGCTCTGGGCCAGGGGCATCCATGGGAGCCCCGTGGGGGGGGGGCCAGGCCAGGCCTCAACGCCCATGTCTTTGCAGCCGAGGAGGAGCTGGTGGAGGCTGACGAGGCGGGCAGTGTGTATGCAGGCATCCTCAGCTACGGGGTGGGCTTCTTCCTGTTCATCCTGGTGGTGGCGGCTGTGACGCTCTGCCGCC\n++\n+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGC?>DFGGFGGGGGGFFFFFFFFFF@FFFFCDFGF?FFAFFFDAAFFBFB9?FFD08<<6?BFFF;F?2<??6??<7>B>9\n+@CCTCCCGGCAGTGCGAAAATGTCA.ba.2\n+CTAGACTCACTGGCGTTACTGACTGCGAGACCCTCCAGACAAGGCGCGTGCTGAGGTTCTGAGCCCCCTTCCGCTCCCAGTGGTGCCTGCGGCTCTGGGCCAGGGGCATCCATGGGAGCCCCGTGGGGGGGGGGCCAGGCCAGGCCTCAACGCCCATGTCTTTGCAGCCGAGGAGGAGCTGGTGGAGGCTGACGAGGCGGGCAGTGTGTATGCAGGCATCCTCAGCTACGGGGTGGGCTTCTTCCTGTTCATCCTGGTGGTGGCGGCTGTGACGCTCTGCCGCC\n++\n+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG=8FGGEGDGGGGGGGGCFFGGGGGGGGGFFFFFFFFFGFFFFB5<BEFB>8AABAFF<9<5FBF?):F:B?:2@FFFF1.54<?:.323<?FF9\n+@CCTCCCGGCAGTGCGAAAATGTCA.ab.2\n+CTAGGCTCTACATGGTGAGCAGAGACGAGGAGAGGGGAGCCCGCCTGGCTGCAGAGAGGGCTCACACAGCCCAGGACCAGTGTGGGCCGAGGTGGGGCTCCAGGAGGCCTGGCGGGCAGGCAGCTCAGAACCTGGTATCTACTTTCTGTTACCTGTCGCTTGAGCGGGAAGCGGGAGATCTTGTGCGCGGTGGGGGAGCCCAGGCCTTTCTTGGGGGGGCTGCGCAGGCGGCAGAGCGTCACAGCCGCCACCACCAGGATGAACAGGAAGAAGCCCACCCCGT\n++\n+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGFFGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGBCGGGGGGGGGGGGGGCFGGGGGGGGEGGEGGGGGGGEGGGGGGGGGGGGGGGDGDDDEFDGGFFGFFFFFGFFFF>EFBFFFGFFFFF:BFFF?F?FFFFFF?F<BBF??BBFFFFBBFF\n+@CCTCCCGGCAGTGCGAAAATGTCA.ba.1\n+CTAGGCTCTACATGGTGAGCAGAGACGAGGAGAGGGGAGCCCGCCTGGCTGCAGAGAGGGCTCACACAGCCCAGGACCAGCGTGGGCCGAGGTGGGGCACCAGGAGGCCTGGCGGGCCGGCAGCTCAGAACCTGATATCTACTTTCTGTTAGCTGTCGCTCGAGCGGGAAGCGGGAGATCTTGTGCGCGGTGTGGGAGCCTAGCCCTTTCTTGGGGTGGCTGCGCAGGCGGCAGAGCGTCACAGCTGCTACAACCAGGATGAACAGGAAGAGCCCCACCCCGTC\n++\n+FCF<9C@F8E9@FGC,,,,<,CF<,C@B@CC@<F,,@F::FD+FC@@F,CFFEEDFGD:C=<<B?FF:E8,B,B,AC<FA8C44++B=>F7F?+A7FF+==<F+:+@7+AFB,8C:F**>CC@F?CCFFCFC@C,26,3224@C@C,,?CG+<+2CFC*:*:);C7E*21*9CE**>DDFC7+:0=/))5C)1)(*)00>*9:(.4(,577:*=47)721),,),(-(4(47()((43460(.)(0..).))).4(()(,(,)6)((((,4((((4(-((((((\n+@CCTCCCGGCAGTGCGAAAATGTCA.ba.1\n+CTAGGCTCTACATGGTGAGCAGAGACGAGGAGAGGGGAGCCCGCCTGGCTGCAGAGAGGGCTCACACAGCCCAGGACCAGCGTGGGCCGAGGTGGGGCTCCAGGAGGCCTGGCGGGCAGGCAGCTCAGAACCTGGTATCTACTTTCTGTTACCTGTCGCTTGAGCGGGAAGCGGGAGATCTTGTGCGCGGTGGGGGAGCCCAGGCCTTTCTTGGGGGGGCTGCGCAGGCGGCAGAGCGTCACAGCCGCCACCACCAGGATGAACAGGAAGCAGCCCAGCCCGT\n++\n+GGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFGGGGGGGGGFGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGGGGGGGGGGGGGFEGDFGFGGGGFGFGGFGGGEG?FGCDGGEGGGGGGGGG6>FEGFDFGGFFGGGEE3DFF@=@FFGF2?>FB9FFFFFBFFFBFFFFFF9>>F>F68?>>?:BABFFFFF6B??:?BF5<>BB<49?:?:?(4?:0:0(.3399\n' |
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| diff -r 3556001ff2db -r 3f1dbd2c59bf test-data/Interesting_Reads_test.trim.bai |
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| Binary file test-data/Interesting_Reads_test.trim.bai has changed |
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| diff -r 3556001ff2db -r 3f1dbd2c59bf test-data/Interesting_Reads_test.trim.bam |
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| Binary file test-data/Interesting_Reads_test.trim.bam has changed |
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| diff -r 3556001ff2db -r 3f1dbd2c59bf test-data/Interesting_Reads_test.trim.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Interesting_Reads_test.trim.fastq Tue Nov 10 12:55:29 2020 +0000 |
| b |
| b'@@ -0,0 +1,120 @@\n+@GATAACCTTGCTTCGTGATTAATC.ab.1\n+CTAGAGGGCCAGACCCTGGAGAGAATGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGTCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCACAGGGCCAGGAGTGAGGGCTCAAGAAGCGGGACGGCCGTAAGTCACAGGATTCCCGTCCGTCCTGGCAGCT\n++\n+GGGGGGGGGGGGGGFGFFGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGAFGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGFGG8<FED@FGEGGGGGGGGGGGGGGGGGGGGGGGGFEFGGGGGGGEEGGGGGGGGGCECE8EGGGEFFGGGGGGFGGGDEDD5EGGGGGFGGGDCFCFGFGFGCFAGGFDFFFEEGGFF3><:>>FD>FFC=4=:0<;DD>6461992<)892<AFBFFFFFF244:-1:1>:=0306(4\n+@GATAACCTTGCTTCGTGATTAATC.ba.2\n+CTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGTCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCACAGGGCCAGGAGGGAGGGCTCAAGAAGCGGGACGGCCGTAAGTCACAGGATTCCCGTCCGTCCTGGCAGCTTTGGCGTGTCCCGAGCCAG\n++\n+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGFGGGGGGGGGGFGGGGGGGGGGGFGGGGGGFCFGGGGFGGGGEGGFGGGGGGGFFGGGGGGGGGGGGGGGGBB?CFGGGGGGCCGGFGGGGGGGCFGECC79CEECGDDD99CFGGGGF4>>GG>BDE@BBFG5=B?AF98::A42<EF?;B::((7:?7???<)/:?91;1,6?F?29902\n+@GATAACCTTGCTTCGTGATTAATC.ba.2\n+CTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGTCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCACAGGGCCAGGAGTGAGGGCTCAAGAAGCGGGACGGCCGTAAGTCACAGGATTCCCGTCCGTCCTGGCAGC\n++\n+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGDGGGGEEGGGGGGGGGGGGGGGGGGGCEFDFGGGFGFGGEGEBFGG<FGFCFEFDFDF<DGGGGGGFGFGFGGGGGFGGGCE:FFBFGGGGDGGGGGGGGDD@FGGFC6AE7E1CGGFGCCFGGGGCEGFGGGCCFG9A*59@FGD><?9=CFF6>3BBDFFF392?G)-96<2<:<:44<232:B3:F>6??F0(3\n+@GATAACCTTGCTTCGTGATTAATC.ba.2\n+CTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACCCCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGTCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCACAGGGCCAGGAGTGA\n++\n+FGEF9FGGCCG@FGGGGGGCFCC@EGGG<FFGGFGGCGGGGGEG?FGGGGDGGGGGGGGFEFGGGGGGGGG7==F:F,=FEGGFFFFG<<F<=8FG>CAF9E8CFCEFFFFF,?F=F8FFD=,DFFE+@CGGGFF7D<FGGEFEGGFG2DCCFGECC*=CGEGGGGGGGGCCFFFGF7FFGFGGGGGGGFFG=E56C55CEGF3:F*9\n+@GATAACCTTGCTTCGTGATTAATC.ab.2\n+GATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTCTCCTTGCACAACGTCACCTTTGAGGACGCCGGGGAGTACACCTGCCTGGCGGGCAATTCTATTGGGTTTTCTCATCACTCTGCGTGGCTGGTGGTGCTGCCAGGTACCGGCTTCTGCTGCTGCTGCTGCTCCGCACTGTCTGGGGGACGCTGGCTCGGGACACG\n++\n+FGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGFGGGGGFFGGGGGGGGGGGGGGGGCFGGFFGGGCGGGGGGGGGCEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDFGGGGGGGGGGGGGGGGGGGGGGGGEGFGGFGFFGFGFGFFBEFGFFFF7F?FFB?DF>FDFFB:)9>FBFFF?F099E>;<?1:<?0>F0;BB1\n+@GATAACCTTGCTTCGTGATTAATC.ba.1\n+GATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTCTCCTTGCACAACGTCACCTTTGAGGACGCCGGGGAGTACACCTGCCTGGCGGGCAATTCTATTGGGTTTTCTCATCACTCTGCGTGGCTGGTGGTGCTGCCAGGTACCGGCTTCTGCTGCTGCTGCTGCTCCGCACTGTCTGGG\n++\n+GGGGGGGGGGGGGGGGGFGGGGGGGGGGGFGGGGGGGGGGGGGGDGGGGGGGGGGGFGGGGGGGGFGGGGGGGGGGGGDGCEEFGGGGGCGGGGGGGGGGGGGFGGGGGGGGFGGGGGGGGGGFGGGCGFFGGGGGGGGGGFFFFGGGGCEG==CECFFCDGGGGGGGGGGGGG597*<FGGFGDFC35>+*:=6FDFF4CFFF9B204>G?FE)5FAF?:7>FBB<A?FB(9?<AFFF<0?B?F4:BFF2>B69>;B))6<<?\n+@GATAACCTTGCTTCGTGATTAATC.ba.1\n+GATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTCTCCTTGCACAACGTCACCTTTGAGGACGCCGGGGAGTACACCTGCCTGGCGGGCAATTCTATTGGGTTTTCTCATCACTCTGCGTGGCTGGTGG\n++\n+FDCCF9FFDFGGGGGGGGGGGGFGGGGGGFGGGGGGGGGGGEGFECFGGGGGGGGGGGGG8EGFGEGFG,F@GGGGGEGGEG7FGGGGG@BFFGCCGGEGGGGGGGFGGGGGGFGGG@FFF9CFGGGGGGGGGGGGGGGGGGGFFGF5E*CECC>EGFGG7EGD==?E8:E7CCE3C+?:C?FFG@D3B5:>78)/C6=FFF<>B>>0:@EBF3\n+@GATTGGATAACGTTGTGGCAATTG.ab.1\n+CTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCACCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGG'..b'ACGCTGGCTCGGGACACGCCAAAGCTGCCAGGACGGACGGGAATCCTGTGACTTACGGCCGTCCCGCTTCTTGAGCCCTCACTCCTGGCCCTGTGCCCAGTGTGGGGACAAAGTTGGCCTGGCCCGGTCCTGGTCCCAGAGGGGCCCCCTCAGCCCCCTCGAG\n++\n+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGEEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGD7FEFBFGGGGGGGCFGGGFGGGGGCGEGGG=CFGGECBFCFACC7DDFGGC9FFGCCFFFFF<@F?FFEGGGGGG8:57ACC=@60;CC:7,CEEGCGG4CFCA<?C<<FGGAFCDC5:>6C?3C.76)03\n+@GATTGGATAACGTTGTGGCAATTG.ba.1\n+GGTACCGGCTTCTGCTGCTGCTGCTGCTCCGCACTGTCTGGGGGACGCTTGCTCGGGACACGCCAAAGCTGCCAGGACGGACGGGAATCCTGTGACTTACGGCCGTCCCGCCTCTTGAGCCCTCACTCCTGGCCCTGTGCCCAGTGTGGGGACAAAGTTGGCCTGGCCCGGTCCTGGTCCCAGAGGGGCCCCCTCA\n++\n+;,EACFFEGD6FFGGG8F<@<FEGGGGGGFCE7F@,EDG9<@:FCFCEF,CFGF>BF6+,9BFA+4EDFFFEFGCC,BFCB:FFGD==C?CFG,,CEE9E7CGGE@FCCGD+8:CC<9DFGG,@:B9:F9BC@5DD5FFG;@DFBCECEE7EC7,,?CFDCDGGGFFFFC://=?=4CF4C+C558DDF5EDGBB5\n+@CCTCCCGGCAGTGCGAAAATGTCA.ab.1\n+CTAGACTCACTGGCGTTACTGACTGCGAGACCCTCCAGACAAGGCGCGTGCTGAGGTTCTGAGCCCCCTTCCGCTCCCAGTGGTGCCTGCGGCTCTGGGCCAGGGGCATCCATGGGAGCCCCGTGGGGGGGGGGGCCAGGCCGGGCCTCAACGCCCAT\n++\n+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG7FGGGGGGGGGGGC<FGGGDGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGDEC8C>C5*:/C:*:<+2/>C:*:\n+@CCTCCCGGCAGTGCGAAAATGTCA.ba.2\n+CTAGACTCACTGGCGTTACTGACTGCGAGACCCTCCAGACAAGGCGCGTGCTGAGGTTCTGAGCCCCCTTCCGCTCCCAGTGGTGCCTGCGGCTCTGGGCCAGGGGCATCCATGGGAGCCCCGTGGGGGGGGGGCCAGGCCAGGCCTCAACGCCCATGTCTTTGCAGCCGAGGAGGAGCTGGTGGAGGCTGAC\n++\n+CFGGAFCFCFGGGFDGDDDGGDGGGG;F:BFGEGFGGGGFF<FFDECG@CFDGGF@FECFAEGFGGGGGAFFEGGGEGF<?E@FFGFEFGEGG+BEF=<FGGCFCFGGGGGGGG8FDFGGDF@FFGGGEEG*88:C88AFEC>8A:@;EFG8>:EEGE0<CCF+<E:CE/C8C*8C*;;C:0*;=EFEDG*/0\n+@CCTCCCGGCAGTGCGAAAATGTCA.ba.2\n+CTAGACTCACTGGCGTTACTGACTGCGAGACCCTCCAGACAAGGCGCGTGCTGAGGTTCTGAGCCCCCTTCCGCTCCCAGTGGTGCCTGCGGCTCTGGGCCAGGGGCATCCATGGGAGCCCCGTGGGGGGGGGGCCAGGCCAGGCCTCAACGCCCATGTCTTTGCAGCCGAGGAGGAGCTGGTGGAGGCTGACGAGGCGGGCAGTGTGTATGCAGGCATCCTCAGCTACGGGGTGGGCTTCTTCCTGTTCATCCTGGTGGTGGCGGCTGTGACGCTCTGCCGCC\n++\n+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGC?>DFGGFGGGGGGFFFFFFFFFF@FFFFCDFGF?FFAFFFDAAFFBFB9?FFD08<<6?BFFF;F?2<??6??<7>B>9\n+@CCTCCCGGCAGTGCGAAAATGTCA.ba.2\n+CTAGACTCACTGGCGTTACTGACTGCGAGACCCTCCAGACAAGGCGCGTGCTGAGGTTCTGAGCCCCCTTCCGCTCCCAGTGGTGCCTGCGGCTCTGGGCCAGGGGCATCCATGGGAGCCCCGTGGGGGGGGGGCCAGGCCAGGCCTCAACGCCCATGTCTTTGCAGCCGAGGAGGAGCTGGTGGAGGCTGACGAGGCGGGCAGTGTGTATGCAGGCATCCTCAGCTACGGGGTGGGCTTCTTCCTGTTCATCCTGGTGGTGGCGGCTGTGACGCTCTGCCGCC\n++\n+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG=8FGGEGDGGGGGGGGCFFGGGGGGGGGFFFFFFFFFGFFFFB5<BEFB>8AABAFF<9<5FBF?):F:B?:2@FFFF1.54<?:.323<?FF9\n+@CCTCCCGGCAGTGCGAAAATGTCA.ab.2\n+CTAGGCTCTACATGGTGAGCAGAGACGAGGAGAGGGGAGCCCGCCTGGCTGCAGAGAGGGCTCACACAGCCCAGGACCAGTGTGGGCCGAGGTGGGGCTCCAGGAGGCCTGGCGGGCAGGCAGCTCAGAACCTGGTATCTACTTTCTGTTACCTGTCGCTTGAGCGGGAAGCGGGAGATCTTGTGCGCGGTGGGGGAGCCCAGGCCTTTCTTGGGGGGGCTGCGCAGGCGGCAGAGCGTCACAGCCGCCACCACCAGGATGAACAGGAAGAAGCCCACCCCGT\n++\n+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGFFGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGBCGGGGGGGGGGGGGGCFGGGGGGGGEGGEGGGGGGGEGGGGGGGGGGGGGGGDGDDDEFDGGFFGFFFFFGFFFF>EFBFFFGFFFFF:BFFF?F?FFFFFF?F<BBF??BBFFFFBBFF\n+@CCTCCCGGCAGTGCGAAAATGTCA.ba.1\n+CTAGGCTCTACATGGTGAGCAGAGACGAGGAGAGGGGAGCCCGCCTGGCTGCAGAGAGGGCTCACACAGCCCAGGACCAGCGTGGGCCGAGGTGGGGCTCCAGGAGGCCTGGCGGGCAGGCAGCTCAGAACCTGGTATCTACTTTCTGTTACCTGTCGCTTGAGCGGGAAGCGGGAGATCTTGTGCGCGGTGGGGGAGCCCAGGCCTTTCTTGGGGGGGCTGCGCAGGCGGCAGAGCGTCACAGCCGCCACCACCAGGATGAACAGGAAGCAGCCCA\n++\n+GGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFGGGGGGGGGFGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGGGGGGGGGGGGGFEGDFGFGGGGFGFGGFGGGEG?FGCDGGEGGGGGGGGG6>FEGFDFGGFFGGGEE3DFF@=@FFGF2?>FB9FFFFFBFFFBFFFFFF9>>F>F68?>>?:BABFFFFF6B??:?BF5<>BB<49?:?:?(4?:0:0\n' |
| b |
| diff -r 3556001ff2db -r 3f1dbd2c59bf test-data/Interesting_Reads_test.trim.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Interesting_Reads_test.trim.log Tue Nov 10 12:55:29 2020 +0000 |
| b |
| @@ -0,0 +1,31 @@ +GATAACCTTGCTTCGTGATTAATC.ab.1 264 0 264 20 +GATAACCTTGCTTCGTGATTAATC.ba.2 283 0 283 1 +GATAACCTTGCTTCGTGATTAATC.ba.2 263 0 263 21 +GATAACCTTGCTTCGTGATTAATC.ba.2 208 0 208 76 +GATAACCTTGCTTCGTGATTAATC.ab.2 284 0 284 0 +GATAACCTTGCTTCGTGATTAATC.ba.1 264 0 264 20 +GATAACCTTGCTTCGTGATTAATC.ba.1 214 0 214 70 +GATTGGATAACGTTGTGGCAATTG.ab.1 185 0 185 99 +GATTGGATAACGTTGTGGCAATTG.ab.1 91 0 91 193 +GATTGGATAACGTTGTGGCAATTG.ab.1 205 0 205 79 +GATTGGATAACGTTGTGGCAATTG.ab.1 233 0 233 51 +GATTGGATAACGTTGTGGCAATTG.ba.2 284 0 284 0 +GATTGGATAACGTTGTGGCAATTG.ba.2 284 0 284 0 +GATTGGATAACGTTGTGGCAATTG.ba.2 237 0 237 47 +GATTGGATAACGTTGTGGCAATTG.ba.2 205 0 205 79 +GATTGGATAACGTTGTGGCAATTG.ba.2 284 0 284 0 +GATTGGATAACGTTGTGGCAATTG.ab.2 252 0 252 32 +GATTGGATAACGTTGTGGCAATTG.ab.2 247 0 247 37 +GATTGGATAACGTTGTGGCAATTG.ab.2 275 0 275 9 +GATTGGATAACGTTGTGGCAATTG.ab.2 282 0 282 2 +GATTGGATAACGTTGTGGCAATTG.ba.1 284 0 284 0 +GATTGGATAACGTTGTGGCAATTG.ba.1 283 0 283 1 +GATTGGATAACGTTGTGGCAATTG.ba.1 207 0 207 77 +GATTGGATAACGTTGTGGCAATTG.ba.1 196 0 196 88 +CCTCCCGGCAGTGCGAAAATGTCA.ab.1 158 0 158 126 +CCTCCCGGCAGTGCGAAAATGTCA.ba.2 193 0 193 91 +CCTCCCGGCAGTGCGAAAATGTCA.ba.2 284 0 284 0 +CCTCCCGGCAGTGCGAAAATGTCA.ba.2 284 0 284 0 +CCTCCCGGCAGTGCGAAAATGTCA.ab.2 283 0 283 0 +CCTCCCGGCAGTGCGAAAATGTCA.ba.1 0 0 0 0 +CCTCCCGGCAGTGCGAAAATGTCA.ba.1 277 0 277 6 |
| b |
| diff -r 3556001ff2db -r 3f1dbd2c59bf test-data/Interesting_Reads_test_data_VA.fastq --- a/test-data/Interesting_Reads_test_data_VA.fastq Wed Dec 04 16:21:17 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,124 +0,0 @@\n-@GATAACCTTGCTTCGTGATTAATC.ab.1\n-CTAGAGGGCCAGACCCTGGAGAGAATGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGTCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCACAGGGCCAGGAGTGAGGGCTCAAGAAGCGGGACGGCCGTAAGTCACAGGATTCCCGTCCGTCCTGGCAGCTTTGGCGTGTCCCGAGCCAGC\n-+\n-GGGGGGGGGGGGGGFGFFGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGAFGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGFGG8<FED@FGEGGGGGGGGGGGGGGGGGGGGGGGGFEFGGGGGGGEEGGGGGGGGGCECE8EGGGEFFGGGGGGFGGGDEDD5EGGGGGFGGGDCFCFGFGFGCFAGGFDFFFEEGGFF3><:>>FD>FFC=4=:0<;DD>6461992<)892<AFBFFFFFF244:-1:1>:=0306(4)-.42((44(667(449?0,\n-@GATAACCTTGCTTCGTGATTAATC.ba.2\n-CTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGTCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCACAGGGCCAGGAGGGAGGGCTCAAGAAGCGGGACGGCCGTAAGTCACAGGATTCCCGTCCGTCCTGGCAGCTTTGGCGTGTCCCGAGCCAGG\n-+\n-GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGFGGGGGGGGGGFGGGGGGGGGGGFGGGGGGFCFGGGGFGGGGEGGFGGGGGGGFFGGGGGGGGGGGGGGGGBB?CFGGGGGGCCGGFGGGGGGGCFGECC79CEECGDDD99CFGGGGF4>>GG>BDE@BBFG5=B?AF98::A42<EF?;B::((7:?7???<)/:?91;1,6?F?29902(\n-@GATAACCTTGCTTCGTGATTAATC.ba.2\n-CTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGTCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCACAGGGCCAGGAGTGAGGGCTCAAGAAGCGGGACGGCCGTAAGTCACAGGATTCCCGTCCGTCCTGGCAGCTTTGGCGTGTCCCGAGCCAGG\n-+\n-GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGDGGGGEEGGGGGGGGGGGGGGGGGGGCEFDFGGGFGFGGEGEBFGG<FGFCFEFDFDF<DGGGGGGFGFGFGGGGGFGGGCE:FFBFGGGGDGGGGGGGGDD@FGGFC6AE7E1CGGFGCCFGGGGCEGFGGGCCFG9A*59@FGD><?9=CFF6>3BBDFFF392?G)-96<2<:<:44<232:B3:F>6??F0(34A248:>?1,(.404-,((4(\n-@GATAACCTTGCTTCGTGATTAATC.ba.2\n-CTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACCCCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGTCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCACAGGGCCAGGAGTGAGGGCTCCAGAAGCGGGACGGCCGTAAGTCCCAGGATTCCCGTCCGTCCTGGCAGCTTTGGCGTGTCCCGAGCCAGC\n-+\n-FGEF9FGGCCG@FGGGGGGCFCC@EGGG<FFGGFGGCGGGGGEG?FGGGGDGGGGGGGGFEFGGGGGGGGG7==F:F,=FEGGFFFFG<<F<=8FG>CAF9E8CFCEFFFFF,?F=F8FFD=,DFFE+@CGGGFF7D<FGGEFEGGFG2DCCFGECC*=CGEGGGGGGGGCCFFFGF7FFGFGGGGGGGFFG=E56C55CEGF3:F*9*./>FG***27)?::D)5557@>BFD@)/))).(().9<2((-29BF>F4(83,:12-)4)2,3??<<1:(7>((,\n-@GATAACCTTGCTTCGTGATTAATC.ab.2\n-GATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTCTCCTTGCACAACGTCACCTTTGAGGACGCCGGGGAGTACACCTGCCTGGCGGGCAATTCTATTGGGTTTTCTCATCACTCTGCGTGGCTGGTGGTGCTGCCAGGTACCGGCTTCTGCTGCTGCTGCTGCTCCGCACTGTCTGGGGGACGCTGGCTCGGGACACG\n-+\n-FGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGFGGGGGFFGGGGGGGGGGGGGGGGCFGGFFGGGCGGGGGGGGGCEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDFGGGGGGGGGGGGGGGGGGGGGGGGEGFGGFGFFGFGFGFFBEFGFFFF7F?FFB?DF>FDFFB:)9>FBFFF?F099E>;<?1:<?0>F0;BB1\n-@GATAACCTTGCTTCGTGATTAATC.ba.1\n-GATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTCTCCTTGCACAACGTCACCTTTGAGGACGCCGGGGAGTACACCTGCCTGGCGGGCAATTCTATTGGGTTTTCTCATCACTCTGCGTGGCTGGTGGTGCTGCCAGGTACCGGCTTCTGCTGCTGCTGCTGCTCCGCACTGTCTGGGGGACGCTGGCGCGGGACACG\n-+\n-GGGGGGGGGGGGGGGGGFGGGGGGGGGGGFGGGGGGGGGGGGGGDGGGGGGGGGGGFGGGGGGGGFGGGGGGGGGGGGDGCEEFGGGGGCGGGGGGGGGGGGGFGGGGGGGGFGGGGGGGGGGFGGGCGFFGGGGGGGGGGFFFFGGGGCEG==CECFFCDGGGGGGGGGGGGG597*<FGGFGDFC35>+*:=6FDFF4CFFF9B204>G?FE)5FAF?:7>FBB<A?FB(9?<AFFF<0?B?F4:BFF2>B69>;B))6<<?(,(46((4,42(7>926(82\n-@GATAACCTTGCTTCGTGATTAATC.ba.1\n-GATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTCTCCTTGCACAACGTCACCTTTGAGGACGCCGGGGAGTACACCTGCCTGGCGGGCAATTCTATTGGGTTTTCTCATCACTCTGCGTGGCTGGTGGTTCTGCCAGGTACCGGCTTCTGCTGCTGCTGCTGCTCCGCACTGTCTGGGGGACGCTGGCCCGGGACACG\n-+\n-FDCCF9FFDFGGGGGGG'..b'CAGGCTCCCTACGCTACGGGGTGGGCTTTTTCCGTTTCATCTTGGTGTTGCCGGCTGGGACGCCTTGCGCC\n-+\n-GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG7FGGGGGGGGGGGC<FGGGDGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGDEC8C>C5*:/C:*:<+2/>C:*:*+*<>?+*+0<5:/>E5<35***<6293*935=DC)))1707C5)(1*))())()*06)(((0,(*(,(,(-4(9),4D6(4((5)4*(,).2))-).5)5:228))-1(-(((((-((,()5(-(\n-@CCTCCCGGCAGTGCGAAAATGTCA.ba.2\n-CTAGACTCACTGGCGTTACTGACTGCGAGACCCTCCAGACAAGGCGCGTGCTGAGGTTCTGAGCCCCCTTCCGCTCCCAGTGGTGCCTGCGGCTCTGGGCCAGGGGCATCCATGGGAGCCCCGTGGGGGGGGGGCCAGGCCAGGCCTCAACGCCCATGTCTTTGCAGCCGAGGAGGAGCTGGTGGAGGCTGACGACGCGGGCAGTGTGTATGCAGTCATCCTCAGCTACGGGCTGGGCTTCTTCCTGTTTATCCTGGTGGTGGCGGCTGTGTCGCTCTGCCGTC\n-+\n-CFGGAFCFCFGGGFDGDDDGGDGGGG;F:BFGEGFGGGGFF<FFDECG@CFDGGF@FECFAEGFGGGGGAFFEGGGEGF<?E@FFGFEFGEGG+BEF=<FGGCFCFGGGGGGGG8FDFGGDF@FFGGGEEG*88:C88AFEC>8A:@;EFG8>:EEGE0<CCF+<E:CE/C8C*8C*;;C:0*;=EFEDG*/0*7*:7*18*27:CFGD?>>7+CGG>?F:?4*7?FG6).-))7)/<BF0)6.)/--/)67.:F209304(((493(,:5-)(2;:<2).4((\n-@CCTCCCGGCAGTGCGAAAATGTCA.ba.2\n-CTAGACTCACTGGCGTTACTGACTGCGAGACCCTCCAGACAAGGCGCGTGCTGAGGTTCTGAGCCCCCTTCCGCTCCCAGTGGTGCCTGCGGCTCTGGGCCAGGGGCATCCATGGGAGCCCCGTGGGGGGGGGGCCAGGCCAGGCCTCAACGCCCATGTCTTTGCAGCCGAGGAGGAGCTGGTGGAGGCTGACGAGGCGGGCAGTGTGTATGCAGGCATCCTCAGCTACGGGGTGGGCTTCTTCCTGTTCATCCTGGTGGTGGCGGCTGTGACGCTCTGCCGCC\n-+\n-GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGC?>DFGGFGGGGGGFFFFFFFFFF@FFFFCDFGF?FFAFFFDAAFFBFB9?FFD08<<6?BFFF;F?2<??6??<7>B>9\n-@CCTCCCGGCAGTGCGAAAATGTCA.ba.2\n-CTAGACTCACTGGCGTTACTGACTGCGAGACCCTCCAGACAAGGCGCGTGCTGAGGTTCTGAGCCCCCTTCCGCTCCCAGTGGTGCCTGCGGCTCTGGGCCAGGGGCATCCATGGGAGCCCCGTGGGGGGGGGGCCAGGCCAGGCCTCAACGCCCATGTCTTTGCAGCCGAGGAGGAGCTGGTGGAGGCTGACGAGGCGGGCAGTGTGTATGCAGGCATCCTCAGCTACGGGGTGGGCTTCTTCCTGTTCATCCTGGTGGTGGCGGCTGTGACGCTCTGCCGCC\n-+\n-GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG=8FGGEGDGGGGGGGGCFFGGGGGGGGGFFFFFFFFFGFFFFB5<BEFB>8AABAFF<9<5FBF?):F:B?:2@FFFF1.54<?:.323<?FF9\n-@CCTCCCGGCAGTGCGAAAATGTCA.ab.2\n-CTAGGCTCTACATGGTGAGCAGAGACGAGGAGAGGGGAGCCCGCCTGGCTGCAGAGAGGGCTCACACAGCCCAGGACCAGTGTGGGCCGAGGTGGGGCTCCAGGAGGCCTGGCGGGCAGGCAGCTCAGAACCTGGTATCTACTTTCTGTTACCTGTCGCTTGAGCGGGAAGCGGGAGATCTTGTGCGCGGTGGGGGAGCCCAGGCCTTTCTTGGGGGGGCTGCGCAGGCGGCAGAGCGTCACAGCCGCCACCACCAGGATGAACAGGAAGAAGCCCACCCCGT\n-+\n-GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGFFGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGBCGGGGGGGGGGGGGGCFGGGGGGGGEGGEGGGGGGGEGGGGGGGGGGGGGGGDGDDDEFDGGFFGFFFFFGFFFF>EFBFFFGFFFFF:BFFF?F?FFFFFF?F<BBF??BBFFFFBBFF\n-@CCTCCCGGCAGTGCGAAAATGTCA.ba.1\n-CTAGGCTCTACATGGTGAGCAGAGACGAGGAGAGGGGAGCCCGCCTGGCTGCAGAGAGGGCTCACACAGCCCAGGACCAGCGTGGGCCGAGGTGGGGCACCAGGAGGCCTGGCGGGCCGGCAGCTCAGAACCTGATATCTACTTTCTGTTAGCTGTCGCTCGAGCGGGAAGCGGGAGATCTTGTGCGCGGTGTGGGAGCCTAGCCCTTTCTTGGGGTGGCTGCGCAGGCGGCAGAGCGTCACAGCTGCTACAACCAGGATGAACAGGAAGAGCCCCACCCCGTC\n-+\n-FCF<9C@F8E9@FGC,,,,<,CF<,C@B@CC@<F,,@F::FD+FC@@F,CFFEEDFGD:C=<<B?FF:E8,B,B,AC<FA8C44++B=>F7F?+A7FF+==<F+:+@7+AFB,8C:F**>CC@F?CCFFCFC@C,26,3224@C@C,,?CG+<+2CFC*:*:);C7E*21*9CE**>DDFC7+:0=/))5C)1)(*)00>*9:(.4(,577:*=47)721),,),(-(4(47()((43460(.)(0..).))).4(()(,(,)6)((((,4((((4(-((((((\n-@CCTCCCGGCAGTGCGAAAATGTCA.ba.1\n-CTAGGCTCTACATGGTGAGCAGAGACGAGGAGAGGGGAGCCCGCCTGGCTGCAGAGAGGGCTCACACAGCCCAGGACCAGCGTGGGCCGAGGTGGGGCTCCAGGAGGCCTGGCGGGCAGGCAGCTCAGAACCTGGTATCTACTTTCTGTTACCTGTCGCTTGAGCGGGAAGCGGGAGATCTTGTGCGCGGTGGGGGAGCCCAGGCCTTTCTTGGGGGGGCTGCGCAGGCGGCAGAGCGTCACAGCCGCCACCACCAGGATGAACAGGAAGCAGCCCAGCCCGT\n-+\n-GGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFGGGGGGGGGFGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGGGGGGGGGGGGGFEGDFGFGGGGFGFGGFGGGEG?FGCDGGEGGGGGGGGG6>FEGFDFGGFFGGGEE3DFF@=@FFGF2?>FB9FFFFFBFFFBFFFFFF9>>F>F68?>>?:BABFFFFF6B??:?BF5<>BB<49?:?:?(4?:0:0(.3399\n' |
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| diff -r 3556001ff2db -r 3f1dbd2c59bf test-data/Interesting_Reads_test_data_VA.trim.bam |
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| diff -r 3556001ff2db -r 3f1dbd2c59bf test-data/SSCS_counts_test.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SSCS_counts_test.json Tue Nov 10 12:55:29 2020 +0000 |
| [ |
| @@ -0,0 +1,1 @@ +[{"ACH_TDII_5regions#570": {"ab": 1, "ba": 1}, "ACH_TDII_5regions#504": {"ab": 2, "ba": 1}, "ACH_TDII_5regions#957": {"ab": 1, "ba": 1}}, {"ACH_TDII_5regions#570": {"ab": 2, "ba": 1}, "ACH_TDII_5regions#504": {"ab": 1, "ba": 1}, "ACH_TDII_5regions#957": {"ab": 1}}] \ No newline at end of file |
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| diff -r 3556001ff2db -r 3f1dbd2c59bf test-data/SSCS_counts_test_data_VA.json --- a/test-data/SSCS_counts_test_data_VA.json Wed Dec 04 16:21:17 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,1 +0,0 @@ -[{"ACH_TDII_5regions#505": {"ab": 2, "ba": 1}, "ACH_TDII_5regions#571": {"ab": 1, "ba": 1}, "ACH_TDII_5regions#958": {"ab": 1, "ba": 1}}, {"ACH_TDII_5regions#505": {"ab": 1, "ba": 1}, "ACH_TDII_5regions#571": {"ab": 2, "ba": 1}, "ACH_TDII_5regions#958": {"ab": 1}}] \ No newline at end of file |
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| diff -r 3556001ff2db -r 3f1dbd2c59bf test-data/SSCS_test.bam |
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| diff -r 3556001ff2db -r 3f1dbd2c59bf test-data/reference.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference.fasta Tue Nov 10 12:55:29 2020 +0000 |
| b |
| @@ -0,0 +1,2 @@ +>ACH_TDII_5regions +GCGGAGGGCCCTCAGCCGCGTGGCGGTGACCAAGTTGGCGGTGGCTGAGGAGTTGGTGGTGGCGGCGTTTTCCTTGCAGCGGCTGGATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGacggcgggcgctaacaccaccgacaaggagctagaggttctctccttgcacaacgtcacctttgaggacgccggggagtacacctgcctggcgggcaattctattgggttttctcatcactctgcgtggctggtggtgctgccagGTACCGGCTTCTGCTGCTGCTGCTGCTCCGCACTGTCTGGGGGACGCTGGCTCGGGACACGCCAAAGCTGCCAGGACGGACGGGAATCCTGTGACTTACGGCCGTCCCGCTTCTTGAGCCCTCACTCCTGGCCCTGTGCCCAGTGTGGGGACAAAGTTGGCCTGGCCCGGTCCTGGTCCCAGAGGGGCCCCCTCAGCCCCCTCGAGCCCACTTCCCATCTGGGTCCCCAAAGGCCTCTCCTGTGGCTCTGGTGTCTCCCGGGCGCCTGGTGGCGGTGTGGGACTGGCTGGCTCTGCTGGGCTCCTTCTCTCCAGGGTCTGGCCCTCTAGACTCACTGGCGTTACTGACTGCGAGACCCTCCAGACAAGGCGCGTGCTGAGGTTCTGAGCCCCCTTCCGCTCCCAGTGGTGCCTGCGGCTCTGGGCCAGGGGCATCCATGGGAGCCCCGTGGGGGGGGGGGCCAGGCCAGGCCTCAACGCCCATGTCTTTGCAGccgaggaggagctggtggaggctgacgaggcgggcagtgtgtatgcaggcatcctcagctacggggtgggcttcttcctgttcatcctggtggtggcggctgtgacgctctgccgcctgcgcagcccccccaagaaaggcctgggctcccccaccgtgcacaagatctcccgcttcccgctcaagcgacagGTAACAGAAAGTAGATACCAGGTTCTGAGCTGCCTGCCCGCCAGGCCTCCTGGAGCCCCACCTCGGCCCACGCTGGTCCTGGGCTGTGTGAGCCCTCTCTGCAGCCAGGCGGGCTCCCCTCTCCTCGTCTCTGCTCACCATGTAGAGCCTAGGGTACTTTGGGGCACGAAACATTCTAAAAATCTTCATTCAATGCTGGTGGAAGTCAGAACGCCCCCCCTTCTGGCCCAGCACTGACCCCCGGCTGTACCTCCACGCCCTGTCGCCCACGCGGCGCCAACCTGCCCCTGCTGACCCAAGCAGgtgtccctggagtccaacgcgtccatgagctccaacacaccactggtgcgcatcgcaaggctgtcctcaggggagggccccacgctggccaatgtctccgagctcgagctgcctgccgaccccaaatgggagctgtctcgggcccgGTCAGTGGTGCTGAGGGCCAGCGTTGGCTGTAGGGGGCTTGGTGGTGGGGGTGAAACAGCCACCAGTCAGAGGCCCGGCTGGGTTTAGGGGCCGTCAGGGATGTGGCGGATGTTGGGTGTGGCTGGGGTTCTGTGGAGATGCTCCTGGGACGGGTGTATGGCAGGGACTGCCCCTCTCAAGGTGCCCTGTCTGGAGGGGCAGCAAGGGCGGGAGGCTGTGGGTGACACTCTTCGTCCTTACGAGCAGGCTGTAGGGGGAGCATGGAGGGCTTCCTGGAGGTGGTGGCTCTGGGCCTCAAGGGCTGGGCCAGGCTGGGGTGGGGACCGTGGTGGGCTGAGAGTGGGCGAGTTTGCACACTCATGGTCCCTCTGCCTCCACTGCCAGgctgaccctgggcaagccccttggggagggctgcttcggccaggtggtcatggcggaggccatcggcattgacaaggaccgggccgccaagcctgtcaccgtagccgtgaagatgctgaaagGTGAGGAGGGGGCGGCCAGGGGTGCAGAGCAGGGCTGGGGGCGCCGCCGCCGCCTGACACAGGCCCCCCGCTCCGTGCACAGacgatgccactgacaaggacctgtcggacctggtgtctgagatggagatgatgaagatgatcgggaaacacaaaaacatcatcaacctgctgggcgcctgcacgcagggcgGTAGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCTCCTGGGCCTGGCAGCCCGTCTGAGGAGCCCGTGTCCCCAGggcccctgtacgtgctggtggagtacgcggccaagggtaacctgcgggagtttctgcgggcgcggcggcccccgggcctggactactccttcgacacctgcaagccgcccgaggagcagctcaccttcaaggacctggtgtcctgtgcctaccaggtggcccggggcatggagtacttggcctcccagaagGTGGGCAGGGCGGCAGGTGTGGGTGGAGTAGGCTGGGCCCTGCCCTGAGATGCTGGGAGCAGCGGGGAGAGGTGGAGAGGCTTCAGCCCTGCCTCCCACCCCTTCCCCAGtgcatccacagggacctggctgcccgcaatgtgctggtgaccgaggacaacgtgatgaagatcgcagacttcgggctggcccgggacgtgcacaacctcgactactacaagaagacgaccaacGTGAGCCCGGCCCTGGGGTGCGGGGGTGGGGGTCATGCCAGTAGGACGCCTGGCGCCAACACCGCCTTCCCACACCCTCCCAGggccggctgcccgtgaagtggatggcgcctgaggccttgtttgaccgagtctacactcaccagagtgacgtGTACGTGTCCTGCAGAGCTCAGGCTTCAGGGGTGGAGGCGGGAACTGGGCAGAGCCAGGACCCCAGCTGCAGTCCCCAGGCCTGTGCCCTGGAGCTCCTGGGTGTGGTTTCTACCCCTCCCTGGGGGCAGCAGCGCAGCCCTGGCCTATTCCCCTGGTGCCCGCCCAGGTGTCTGTCCTGGGAGTCTCAGGACAGCCTGACCTCACCTTCCCCTGCAGctggtcctttggggtcctgctctgggagatcttcacgctggggggctccccgtaccccggcatccctgtggaggagctcttcaagctgctgaaggagggccaccgcatggacaagcccgccaactgcacacacgacctGTGAGTGGCATCCCTG |
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| diff -r 3556001ff2db -r 3f1dbd2c59bf test-data/tag_count_dict_test.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tag_count_dict_test.json Tue Nov 10 12:55:29 2020 +0000 |
| [ |
| @@ -0,0 +1,1 @@ +[{"GATAACCTTGCTTCGTGATTAATC": {"ACH_TDII_5regions#504": "A"}, "GATTGGATAACGTTGTGGCAATTG": {"ACH_TDII_5regions#570": "T"}, "CCTCCCGGCAGTGCGAAAATGTCA": {"ACH_TDII_5regions#957": "C"}}, {"ACH_TDII_5regions#570": [1, 1, 143.0], "ACH_TDII_5regions#504": [1, 1, 173.0], "ACH_TDII_5regions#957": [0, 1, 195.0]}] \ No newline at end of file |
| b |
| diff -r 3556001ff2db -r 3f1dbd2c59bf test-data/tag_count_dict_test_data_VA.json --- a/test-data/tag_count_dict_test_data_VA.json Wed Dec 04 16:21:17 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,1 +0,0 @@ -[{"GATAACCTTGCTTCGTGATTAATC": {"ACH_TDII_5regions#505": "A"}, "GATTGGATAACGTTGTGGCAATTG": {"ACH_TDII_5regions#571": "T"}, "CCTCCCGGCAGTGCGAAAATGTCA": {"ACH_TDII_5regions#958": "C"}}, {"ACH_TDII_5regions#505": [1, 1, 173.0], "ACH_TDII_5regions#571": [1, 1, 143.0], "ACH_TDII_5regions#958": [0, 1, 195.0]}] \ No newline at end of file |
| b |
| diff -r 3556001ff2db -r 3f1dbd2c59bf va_macros.xml --- a/va_macros.xml Wed Dec 04 16:21:17 2019 -0500 +++ b/va_macros.xml Tue Nov 10 12:55:29 2020 +0000 |
| b |
| @@ -2,19 +2,20 @@ <xml name="citation"> <citations> <citation type="bibtex"> -@misc{duplex, - author = {Povysil, Gundula and Heinzl, Monika and Salazar, Renato and Stoler, Nicholas and Nekrutenko, Anton and Tiemann-Boege, Irene}, - year = {2019}, - title = {{Variant Analyzer: a quality control for variant calling in duplex sequencing data (manuscript)}} - } - </citation> + @misc{duplex, + author = {Povysil, Gundula and Heinzl, Monika and Salazar, Renato and Stoler, Nicholas and Nekrutenko, Anton and Tiemann-Boege, Irene}, + year = {2020}, + title = {{Increased yields of duplex sequencing data by a series of quality control tools (manuscript)}} + } + </citation> </citations> </xml> <xml name="requirements"> <requirements> - <requirement type="package" version="3.1.2">matplotlib</requirement> - <requirement type="package" version="0.15">pysam</requirement> - <yield/> + <requirement type="package" version="3.1.2">matplotlib</requirement> + <requirement type="package" version="0.15">pysam</requirement> + <requirement type="package" version="0.11.6">cyvcf2</requirement> + <yield/> </requirements> </xml> -</macros> +</macros> \ No newline at end of file |