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Changeset 8:c24910ad5441 (2019-03-28)

Previous changeset 7:192bd5b78300 (2019-01-21) Next changeset 9:0bc56f894766 (2019-08-16)

Commit message:
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b

modified:
test-data/hg19_chrM.fa
test-data/test-cache/hg19_chrM.fa
varscan.py

added:
test-data/high_cov_chrM.bam

diff -r 192bd5b78300 -r c24910ad5441 test-data/hg19_chrM.fa
--- a/test-data/hg19_chrM.fa Mon Jan 21 12:06:22 2019 -0500
+++ b/test-data/hg19_chrM.fa Thu Mar 28 18:19:36 2019 -0400

@@ -1,5 +1,5 @@
>chrM
-GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCAT
+NNNCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCAT
TTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTG
GAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATT
CTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACCTACTA

diff -r 192bd5b78300 -r c24910ad5441 test-data/high_cov_chrM.bam

Binary file test-data/high_cov_chrM.bam has changed

diff -r 192bd5b78300 -r c24910ad5441 test-data/test-cache/hg19_chrM.fa
--- a/test-data/test-cache/hg19_chrM.fa Mon Jan 21 12:06:22 2019 -0500
+++ b/test-data/test-cache/hg19_chrM.fa Thu Mar 28 18:19:36 2019 -0400

diff -r 192bd5b78300 -r c24910ad5441 varscan.py
--- a/varscan.py Mon Jan 21 12:06:22 2019 -0500
+++ b/varscan.py Thu Mar 28 18:19:36 2019 -0400

[

b'@@ -402,7 +402,12 @@\n """Add standard FORMAT key declarations to a VCF header."""\n \n format_field_specs = [\n- (\'GT\', \'1\', \'String\', \'Genotype\'),\n+ # pysam will not add quotes around single-word descriptions,\n+ # which is a violation of the VCF specification.\n+ # To work around this we are using two words as the\n+ # GT format description (instead of the commonly used "Genotype").\n+ # This could be changed once pysam learns to quote correctly.\n+ (\'GT\', \'1\', \'String\', \'Genotype code\'),\n (\'GQ\', \'1\', \'Integer\', \'Genotype quality\'),\n (\'DP\', \'1\', \'Integer\', \'Read depth\'),\n (\'AD\', \'R\', \'Integer\', \'Read depth for each allele\'),\n@@ -423,24 +428,7 @@\n header.merge(temp_header)\n \n def _compile_common_header(self, varcall_template, no_filters=False):\n- # fix the header generated by VarScan\n- # by adding reference and contig information\n- common_header = pysam.VariantHeader()\n- common_header.add_meta(\'reference\', value=self.ref_genome)\n- self._add_ref_contigs_to_header(common_header)\n- if not no_filters:\n- # add filter info\n- self._add_filters_to_header(common_header)\n- # change the source information\n- common_header.add_meta(\'source\', value=\'varscan.py\')\n- # declare an INDEL flag for record INFO fields\n- self._add_indel_info_flag_to_header(common_header)\n- # generate standard FORMAT field declarations\n- # including a correct AD declaration to prevent VarScan\'s\n- # non-standard one from getting propagated\n- self._standardize_format_fields(common_header)\n- # take the remaining metadata from the template header produced by\n- # VarScan\n+ # read the header produced by VarScan for use as a template\n with pysam.VariantFile(varcall_template, \'r\') as original_data:\n varscan_header = original_data.header\n # don\'t propagate non-standard and redundant FORMAT keys written\n@@ -449,9 +437,29 @@\n varscan_header.formats.remove_header(\'FREQ\')\n varscan_header.formats.remove_header(\'RD\')\n varscan_header.formats.remove_header(\'DP4\')\n+ # build a new header containing information not written by VarScan\n+ common_header = pysam.VariantHeader()\n+ # copy over sample info from the VarScan template\n for sample in varscan_header.samples:\n common_header.samples.add(sample)\n+ # add reference information\n+ common_header.add_meta(\'reference\', value=self.ref_genome)\n+ # change the source information\n+ common_header.add_meta(\'source\', value=\'varscan.py\')\n+ # add contig information\n+ self._add_ref_contigs_to_header(common_header)\n+ # declare an INDEL flag for record INFO fields\n+ self._add_indel_info_flag_to_header(common_header)\n+ # merge in remaining information from the VarScan template\n common_header.merge(varscan_header)\n+ # add additional FILTER declarations\n+ if not no_filters:\n+ # add filter info\n+ self._add_filters_to_header(common_header)\n+ # generate standard FORMAT field declarations\n+ # including a correct AD declaration to prevent VarScan\'s\n+ # non-standard one from getting propagated\n+ self._standardize_format_fields(common_header)\n return common_header\n \n def _fix_record_gt_fields(self, record):\n@@ -498,54 +506,12 @@\n del record.format[\'RD\']\n del record.format[\'DP4\']\n \n- def pileup_masker(self, mask):\n- def apply_mask_on_pileup(piled_items):\n- for item, status in zip(piled_items, mask):\n- if status:\n- yield item\n- return apply_mask_on_pileup\n-\n def get_allele_specific_pileup_column_stats(\n- self, allele, pile_column, ref_fetch\n+ self, allele, pile_colum'..b"alse\n+ if use_md:\n+ # The ref sequence got calculated from alignment and MD tag.\n+ for qpos, rpos, ref_base in aligned_pairs:\n+ # pysam uses lowercase ref bases to indicate mismatches\n+ if (\n+ ref_base == 'a' or ref_base == 't' or\n+ ref_base == 'g' or ref_base == 'c'\n+ ):\n+ sum_num_mismatches += 1\n+ sum_mismatch_qualities += p.alignment.query_qualities[\n+ qpos\n+ ]\n+ else:\n+ # We need to obtain the aligned portion of the reference\n+ # sequence.\n+ aligned_pairs = p.alignment.get_aligned_pairs(\n+ matches_only=True\n+ )\n+ # note that ref bases can be lowercase\n+ ref_seq = ref_fetch(\n+ aligned_pairs[0][1], aligned_pairs[-1][1] + 1\n+ ).upper()\n+ ref_offset = aligned_pairs[0][1]\n+\n+ for qpos, rpos in p.alignment.get_aligned_pairs(\n+ matches_only=True\n+ ):\n+ # see if we have a mismatch to the reference at this\n+ # position, but note that\n+ # - the query base may be lowercase (SAM/BAM spec)\n+ # - an '=', if present in the query seq, indicates a match\n+ # to the reference (SAM/BAM spec)\n+ # - there cannot be a mismatch with an N in the reference\n+ ref_base = ref_seq[rpos - ref_offset]\n+ read_base = p.alignment.query_sequence[qpos].upper()\n+ if (\n+ read_base != '=' and ref_base != 'N'\n+ ) and (\n+ ref_base != read_base\n+ ):\n sum_num_mismatches += 1\n sum_mismatch_qualities += p.alignment.query_qualities[\n qpos\n@@ -582,7 +619,13 @@\n sum_num_mismatches_as_fraction += (\n sum_num_mismatches / p.alignment.query_alignment_length\n )\n- avg_basequality = sum_avg_base_qualities / var_reads_total\n+\n+ var_reads_total = var_reads_plus + var_reads_minus\n+ if var_reads_total == 0:\n+ # No stats without reads!\n+ return None\n+ avg_mapping_quality = sum_mapping_qualities / var_reads_total\n+ avg_basequality = sum_base_qualities / var_reads_total\n avg_pos_as_fraction = sum_dist_from_center / var_reads_total\n avg_num_mismatches_as_fraction = (\n sum_num_mismatches_as_fraction / var_reads_total\n@@ -643,6 +686,10 @@\n # skip indel postprocessing for the moment\n yield record\n continue\n+ if record.alleles[0] == 'N':\n+ # It makes no sense to call SNPs against an unknown\n+ # reference base\n+ continue\n # get pileup for genomic region affected by this variant\n if record.info['SS'] == '2':\n # a somatic variant => generate pileup from tumor data\n@@ -825,12 +872,15 @@\n except Exception:\n pass\n \n- def noop_gen(data, **kwargs):\n- for d in data:\n- yield d\n+ def filter_minimal(data, **kwargs):\n+ for record in data:\n+ if record.alleles[0] != 'N' or len(record.alleles[1]) > 1:\n+ # Yield everything except SNPs called against an unknown\n+ # reference base\n+ yield record\n \n if no_filters:\n- apply_filters = noop_gen\n+ apply_filters = filter_minimal\n else:\n apply_filters = self._postprocess_variant_records\n \n"