README
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Bioinformatics tools
- bio-fusion: High-performance RNA/DNA fusion detector
Infrastructure libraries
- encoding/bamprovider: Parallel BAM/PAM reader and parallel paired reader.
- encoding/fasta: FASTA reader and writer.
- encoding/fastq: FASTQ reader
- encoding/pam: A faster, smaller alternative to BAM files.
- encoding/bam: Utilities for BAM files. Based on github.com/biogo/hts.
- encoding/converter: Conversion between file formats
- cmd/bio-pamtool: "samtool" like tool for PAM and BAM.
- cmd/bio-bam-sort: Tool for sorting and merging aligner outputs into PAM or BAM.
- cmd/bio-bam-gindex: Alternate index for faster seeking into BAM files.
- cmd/bio-pileup: Tool to support variant calling on PAM or BAM.
- biosimd: Fast reverse-complement, pack/unpack from BAM seq[] format, etc.
Directories
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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.
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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. |
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Package circular provides sliding-window data structures which are frequently useful when iterating through sorted BAM/PAM/BED files.
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Package circular provides sliding-window data structures which are frequently useful when iterating through sorted BAM/PAM/BED files. |
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cmd
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bio-bam-gindex
Command bio-bam-gindex reads a .bam file and writes a .gbai index file.
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Command bio-bam-gindex reads a .bam file and writes a .gbai index file. |
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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.
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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. |
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encoding
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bam
Package bam provides types and functions that augment BAM and SAM packages in github.com/biogo/hts.
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Package bam provides types and functions that augment BAM and SAM packages in github.com/biogo/hts. |
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bampair
Package bampair provides a way to get the mate of each read when reading a BAM/PAM file that is sorted by position.
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Package bampair provides a way to get the mate of each read when reading a BAM/PAM file that is sorted by position. |
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bamprovider
Package bamprovider provider utilities for scanning a BAM/PAM file in parallel.
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Package bamprovider provider utilities for scanning a BAM/PAM file in parallel. |
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bgzf
Package bgzf includes a Writer for the .bgzf (block gzipped) file format.
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Package bgzf includes a Writer for the .bgzf (block gzipped) file format. |
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fasta
Package fasta contains code for parsing (optionally indexed) FASTA files.
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Package fasta contains code for parsing (optionally indexed) FASTA files. |
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fastq
Package fastq provides code for working with FASTQ format data.
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Package fastq provides code for working with FASTQ format data. |
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pam
Package pam implements PAM reader and writer.
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Package pam implements PAM reader and writer. |
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pam/fieldio
Package fieldio provides a reader and a writer for individual column (field).
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Package fieldio provides a reader and a writer for individual column (field). |
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cmd
This is the main package for parsegencode.
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This is the main package for parsegencode. |
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parsegencode
Package parsegencode contains the required methods for parsing a gencode GTF annotation and printing out the transcripts to an output file.
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Package parsegencode contains the required methods for parsing a gencode GTF annotation and printing out the transcripts to an output file. |
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Package interval implements interval-union operations in a manner optimized for sets of genomic coordinates represented by BED files.
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Package interval implements interval-union operations in a manner optimized for sets of genomic coordinates represented by BED files. |
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