dhtslib

Modules

bgzf

module dhtslib.bgzf

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.

cigar

module dhtslib.cigar

This module simplifies working with CIGAR strings/ops from SAM/BAM/CRAM alignment records.

md

module dhtslib.md

Module to deal with SAM records' MD auxillary tag.

sam

module dhtslib.sam

SAMRecord and SAMFile are wrappers for htslib functions relating to SAM/BAM/CRAM* files

tabix

module dhtslib.tabix

Module providing a wrapper, TabixIndexedFile over a line-oriented NGS flat file, such as BED, GFF3, VCF that has been indexed with tabix.

tagvalue

module dhtslib.tagvalue

Module provides a parser for SAM/BAM record auxillary tags.

vcf

module dhtslib.vcf

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).

Public Imports

dhtslib.bgzf

public import dhtslib.bgzf;

dhtslib.cigar

public import dhtslib.cigar;

dhtslib.faidx

public import dhtslib.faidx;

dhtslib.sam

public import dhtslib.sam;

dhtslib.tabix

public import dhtslib.tabix;

dhtslib.tagvalue

public import dhtslib.tagvalue;

dhtslib.vcf

public import dhtslib.vcf;

• dhtslib
• htslib
• test