constants module

mavis.validate.constants.VALIDATION_DEFAULTS = Namespace(assembly_include_flanking_pairs=True, assembly_include_half_mapped_reads=True, assembly_max_kmer_size=None, assembly_max_kmer_strict=True, assembly_max_paths=20, assembly_min_edge_weight=3, assembly_min_exact_match_to_remap=4, assembly_min_remapped_seq=3, assembly_min_tgt_to_exclude_half_map=7, assembly_strand_concordance=0.51, blat_min_identity=0.9, blat_min_percent_of_max_score=0.8, blat_min_query_consumption=0.7, call_error=10, consensus_req=3, fetch_reads_bins=3, fetch_reads_limit=3000, 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=3, min_linking_split_reads=2, min_mapping_quality=20, min_non_target_aligned_split_reads=1, min_sample_size_to_apply_percentage=10, min_softclipping=6, min_spanning_reads_resolution=3, min_splits_reads_resolution=3, sc_extension_stop=5, stdev_count_abnormal=3, strand_determining_read=2)

Namespace – holds the settings for computations with the Evidence objects

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

when building the initial deBruijn graph edge weights are determined by the frequency of the kmer they represent in all the input sequences. The parameter here discards edges to the kmer they represent in all the input sequences. The parameter here discards edges to simply the graph if they have a weight less than specified

assembly_min_remap

The minimum input sequences that must remap for an assembly 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

blat_min_query_consumption

minimum fraction of the original query sequence that must be used by the read(s) of the alignment

call_error

buffer zone for the evidence window

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_resolutionraw_break1_half_mapped_reads

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

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