Crate noodles 

noodles attempts to provide specification-compliant (when applicable) implementations of libraries for handling various bioinformatics file formats. It currently supports BAM 1.6, BCF 2.2, BED, BGZF, CRAM 3.0/3.1, CSI, FASTA, FASTQ, GFF3, GTF 2.2, htsget 1.3, refget 2.0, SAM 1.6, tabix, and VCF 4.3/4.4.

Modules

bam

noodles-bam handles the reading and writing of the BAM (Binary Alignment/Map) file format.

bcf

noodles-bcf handles the reading and writing of the BCF format.

bed

noodles-bed handles the reading and writing of the BED (Browser Extensible Data) format.

bgzf

noodles-bgzf handles the reading and writing of the blocked gzip format (BGZF).

core

noodles-core contains shared structures and behavior among noodles libraries.

cram

noodles-cram handles the reading and writing of the CRAM format.

csi

noodles-csi handles the reading and writing of the coordinate-sorted index (CSI) format.

fasta

noodles-fasta handles and reading and writing of the FASTA format.

fastq

noodles-fastq handles the reading and writing of the FASTQ format.

gff

noodles-gff handles the reading and writing of the GFF3 format.

gtf

noodles-gtf handles the reading and writing of the Gene Transfer Format (GTF).

htsget

noodles-htsget is an htsget 1.3 client.

refget

noodles-refget is a refget 2.0 client.

sam

noodles-sam handles the reading and writing of the SAM (Sequence Alignment/Map) format.

tabix

noodles-tabix handles the reading and writing of the tabix format.

vcf

noodles-vcf handles the reading and writing of the VCF format.