grailbio

module
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Published: Mar 1, 2024 License: Apache-2.0

README

Bioinformatics tools

  • bio-fusion: High-performance RNA/DNA fusion detector

Infrastructure libraries

Directories

Path Synopsis
Package biosimd provides access to SIMD-based implementations of several common .bam/.fa/etc.-specific operations on byte arrays which the compiler cannot be trusted to autovectorize within the next several years.
Package biosimd provides access to SIMD-based implementations of several common .bam/.fa/etc.-specific operations on byte arrays which the compiler cannot be trusted to autovectorize within the next several years.
Package circular provides sliding-window data structures which are frequently useful when iterating through sorted BAM/PAM/BED files.
Package circular provides sliding-window data structures which are frequently useful when iterating through sorted BAM/PAM/BED files.
cmd
bio-bam-gindex
Command bio-bam-gindex reads a .bam file and writes a .gbai index
Command bio-bam-gindex reads a .bam file and writes a .gbai index
bio-pileup
Given a BAM or PAM, and a BED file describing genomic positions of interest, bio-pileup reports the number of reads supporting each allele at each position.
Given a BAM or PAM, and a BED file describing genomic positions of interest, bio-pileup reports the number of reads supporting each allele at each position.
encoding
bam
Package bam provides types and functions that augment BAM and SAM packages in github.com/biogo/hts.
Package bam provides types and functions that augment BAM and SAM packages in github.com/biogo/hts.
bampair
Package bampair provides a way to get the mate of each read when
Package bampair provides a way to get the mate of each read when
bamprovider
Package bamprovider provider utilities for scanning a BAM/PAM file in parallel.
Package bamprovider provider utilities for scanning a BAM/PAM file in parallel.
bgzf
Package bgzf includes a Writer for the .bgzf (block gzipped) file format.
Package bgzf includes a Writer for the .bgzf (block gzipped) file format.
fasta
Package fasta contains code for parsing (optionally indexed) FASTA files.
Package fasta contains code for parsing (optionally indexed) FASTA files.
fastq
Package fastq provides code for working with FASTQ format data.
Package fastq provides code for working with FASTQ format data.
pam
Package pam implements PAM reader and writer.
Package pam implements PAM reader and writer.
pam/fieldio
Package fieldio provides a reader and a writer for individual column (field).
Package fieldio provides a reader and a writer for individual column (field).
cmd
This is the main package for parsegencode.
This is the main package for parsegencode.
parsegencode
Package parsegencode contains the required methods for parsing a gencode GTF annotation and printing out the transcripts to an output file.
Package parsegencode contains the required methods for parsing a gencode GTF annotation and printing out the transcripts to an output file.
Package interval implements interval-union operations in a manner optimized
Package interval implements interval-union operations in a manner optimized
snp

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