dhtslib ~bam_writing

dhtslib

Overview

D bindings and convenience wrappers for htslib

Installation

Add dhtslib as a dependency to dub.json:

    "dependencies": {
        "dhtslib": "~>0.5.0",

(version number 0.5.0 is example but current as of today)

Usage

Convenience Wrappers

Object-oriented, idomatic(ish) D wrappers are available for:

• BGZF compressed files (dhtslib.bgzf)
• FASTA indexes (dhtslib.faidx)
• SAM/BAM/CRAM files and streams (dhtslib.sam)
• Tabix-indexed files (dhtslib.tabix)
• VCF/BCF files (dhtslib.vcf)

For example, this provides access to BGZF files by line as a consumable InputRange. Or, for BAM files, the ability to query for a range (e.g. "chr1:1000000-2000000") and obtain an InputRange over the BAM records.

htslib API

Direct bindings to htslib C API are available as submodules under dhtslib.htslib. Naming remains the same as the original .h include files. For example, import dhtslib.htslib.faidx for direct access to the C function calls. The current compatible versions are 1.7-1.9.

Currently implemented fully or partially:

• bgzf
• faidx
• hts
• hts_log
• kstring
• regidx
• sam
• tbx
• thread_pool (untested)
• vcf

Missing (so far):

• Some CRAM specific functions, although much CRAM functionality works with sam_ functions
• hfile
• kbitset, kfunc, khash, klist, knetfile, kseq, ksort (mostly used internally anyway)
• syncedbcfreader
• vcf_sweep
• vcfutils

Bugs and Warnings

Do not call htslog htslog_* from a destructor, as it is potentialy allocating via toStringz