This module provides a wrapper, BGZFile, over an htslib BGZF compressed file/stream. The wrapper acts as a linewise ForwardRange over the file or stream.
This module simplifies working with CIGAR strings/ops from SAM/BAM/CRAM alignment records.
This module provides a wrapper, IndexedFastaFile over a FASTA. If an index exists, it will be used for rapid random access. If an index does not exist, one will be built.
Module to deal with SAM records' MD auxillary tag.
SAMRecord and SAMFile are wrappers for htslib functions relating to SAM/BAM/CRAM* files
Module providing a wrapper, TabixIndexedFile over a line-oriented NGS flat file, such as BED, GFF3, VCF that has been indexed with tabix.
Module provides a parser for SAM/BAM record auxillary tags.
VCF version 4.2 (including BCF) reader and writer, including a model with convenience functions for the header (metadata) and individual VCF/BCF records (rows).