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.