align module¶
Should take in a sam file from a aligner like bwa aln or bwa mem and convert it into a
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mavis.align.
align_contigs
(evidence, INPUT_BAM_CACHE, reference_genome, blat_min_percent_of_max_score=0.8, blat_min_identity=0.7, aligner='blat', aligner_output_file='blat_out.pslx', aligner_fa_input_file='blat_in.fa', aligner_reference='/home/pubseq/genomes/Homo_sapiens/GRCh37/blat/hg19.2bit', contig_aln_min_query_consumption=0.5, contig_aln_max_event_size=50, contig_aln_min_anchor_size=50, contig_aln_merge_inner_anchor=20, contig_aln_merge_outer_anchor=20, is_protein=False, min_extend_overlap=10, pair_scoring_function=<function paired_alignment_score>, clean_files=True, log=<function devnull>, **kwargs)[source]¶ given a set of contigs, call the aligner from the command line and adds the results to the contigs asscoated with each Evidence object
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mavis.align.
query_coverage_interval
(read)[source]¶ Returns: The portion of the original query sequence that is aligned by this read Return type: Interval
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mavis.align.
select_paired_alignments
(bpp, aligned_contigs, min_query_consumption, min_extend_overlap, max_event_size, min_anchor_size, merge_inner_anchor, merge_outer_anchor)[source]¶ give a breakpoint pair and a set of alignments for contigs associated with the given pair, alignments are paired (some events cannot be represented with a single bamfile alignment) and the most appropriate alignments supporting the breakpoint pair are selected and returned