galaxy.visualization.data_providers package¶
Galaxy visualization/visual analysis data providers.
Subpackages¶
Submodules¶
galaxy.visualization.data_providers.basic module¶
galaxy.visualization.data_providers.cigar module¶
Functions for working with SAM/BAM CIGAR representation.
- galaxy.visualization.data_providers.cigar.get_ref_based_read_seq_and_cigar(read_seq, read_start, ref_seq, ref_seq_start, cigar)[source]¶
Returns a ( new_read_seq, new_cigar ) that can be used with reference sequence to reconstruct the read. The new read sequence includes only bases that cannot be recovered from the reference: mismatches and insertions (soft clipped bases are not included). The new cigar replaces Ms with =s and Xs because the M operation can denote a sequence match or mismatch.