constants module¶

mavis.validate.constants.DEFAULTS = MavisNamespace(aligner='blat', assembly_include_flanking_pairs=True, assembly_include_half_mapped_reads=True, assembly_max_kmer_size=None, assembly_max_kmer_strict=True, assembly_max_paths=4, assembly_min_edge_weight=2, assembly_min_exact_match_to_remap=4, assembly_min_nc_edge_weight=4, assembly_min_remap_coverage=0.9, assembly_min_remapped_seq=3, assembly_min_tgt_to_exclude_half_map=7, assembly_min_uniq=0.01, assembly_strand_concordance=0.51, blat_limit_top_aln=10, blat_min_identity=0.9, call_error=10, consensus_req=3, contig_aln_max_event_size=50, contig_aln_merge_inner_anchor=20, contig_aln_merge_outer_anchor=15, contig_aln_min_anchor_size=50, contig_aln_min_query_consumption=0.9, fetch_method_individual=True, fetch_min_bin_size=50, fetch_reads_bins=5, fetch_reads_limit=10000, filter_secondary_alignments=True, fuzzy_mismatch_number=1, max_sc_preceeding_anchor=6, min_anchor_exact=6, min_anchor_fuzzy=10, min_anchor_match=0.9, min_double_aligned_to_estimate_insertion_size=2, min_flanking_pairs_resolution=10, min_linking_split_reads=2, min_mapping_quality=5, min_non_target_aligned_split_reads=1, min_sample_size_to_apply_percentage=10, min_softclipping=6, min_spanning_reads_resolution=5, min_splits_reads_resolution=3, outer_window_min_event_size=125, sc_extension_stop=5, stdev_count_abnormal=3.0, strand_determining_read=2)¶

MavisNamespace – holds the settings for computations with the Evidence objects

aligner: the aligner to use to map the contigs/reads back to the reference e.g blat or bwa
assembly_include_flanking_pairs: if true then when the split reads are assembled, any flanking read pairs will also be added
assembly_max_kmer_size: the minimum between this and the smallest length input sequence is used as the kmer size for assembling the DeBruijn Graph. If this is not set the default is the 75% of the minimum length input sequence
assembly_max_kmer_strict: if set to True then any sequences input to the assembly algorithm that cannot create a kmer of this size will be discard. However, if this is set to False, then the kmer size will be reduced accordingly and all input sequences will be used in the assembly algorithm
assembly_max_paths: the maximum number of paths to resolve. This is used to limit when there is a messy assembly graph to resolve. The assembly will pre-calculate the number of paths (or putative assemblies) and stop if it is greater than the given setting.
assembly_min_edge_weight: Discards all edges with a weight/frequency less than this from the DeBruijn graph
assembly_min_nc_edge_weight: Discards all non-cutting edges with a weight/frequency less than this from the DeBruijn graph
assembly_min_remap_coverage: minimum fraction of the contig sequence which the remapped sequences must align over
assembly_min_remapped_seq: The minimum input sequences that must remap for an assembled contig to be used
assembly_strand_concordance: when the number of remapped reads from each strand are compared, the ratio must be above this number to decide on the strand
blat_min_identity: the minimum percent identity match required for blat results when aligning contigs
blat_min_percent_of_max_score: filter based on blat score values. The best match, highest score, is used as the top value and other results must be at least this fraction of the maximum score or they are filtered out
call_error: buffer zone for the evidence window
contig_aln_max_event_size: relates to determining breakpoints when pairing contig alignments. For any given read in a putative pair the soft clipping is extended to include any events of greater than this size. The softclipping is added to the side of the alignment as indicated by the breakpoint we are assigning pairs to
contig_aln_merge_inner_anchor: the minimum number of consecutive exact match base pairs to not merge events within a contig alignment
contig_aln_min_anchor_size: the minimum number of aligned bases for a contig (M or =) in order to simplify. Do not have to be consecutive.
contig_aln_min_exact_block_event_merge: the minimum number of exact matches in a read cigar string to stop merging on “events”. Events meaning insertions, deletions, and mismatches
contig_aln_min_query_consumption: minimum fraction of the original query sequence that must be used by the read(s) of the alignment
fetch_min_bin_size: the minimum size of any bin for reading from a bam file. Increasing this number will result in smaller bins being merged or less bins being created (depending on the fetch method)
fetch_reads_bins: number of bins to split an evidence window into to ensure more even sampling of high coverage regions
fetch_reads_limit: maximum number of reads, cap, to loop over for any given evidence window
filter_secondary_alignments: filter secondary alignments when gathering read evidence
max_sc_preceeding_anchor: when remapping a softclipped read this determines the amount of softclipping allowed on the side opposite of where we expect it. For example for a softclipped read on a breakpoint with a left orientation this limits the amount of softclipping that is allowed on the right. If this is set to None then there is no limit on softclipping
median_fragment_size: the median insert size of paired end reads
min_double_aligned_to_estimate_insertion_size: The minimum number of reads which map soft-clipped to both breakpoints to assume the size of the untemplated sequence between the breakpoints is at most the read length - 2 * min_softclipping
min_flanking_pairs_resolution: the minimum number of flanking reads required to call a breakpoint by flanking evidence
min_linking_split_reads: The minimum number of split reads which aligned to both breakpoints
min_mapping_quality: the minimum mapping quality of reads to be used as evidence
min_non_target_aligned_split_reads: The minimum number of split reads aligned to a breakpoint by the input bam and no forced by local alignment to the target region to call a breakpoint by split read evidence
min_softclipping: minimum number of soft-clipped bases required for a read to be used as soft-clipped evidence
min_splits_reads_resolution: minimum number of split reads required to call a breakpoint by split reads
outer_window_min_event_size: the minimum size of an event in order for flanking read evidence to be collected
read_length: length of reads in the bam file
stdev_count_abnormal: the number of standard deviations away from the normal considered expected and therefore not qualifying as flanking reads
stdev_fragment_size: the standard deviation in insert sizes of paired end reads
strand_determining_read: 1 or 2. The read in the pair which determines if (assuming a stranded protocol) the first or second read in the pair matches the strand sequenced