Converters between equivalent formats: SAM/BAM and FASTA/TwoBit.
Converters between equivalent formats: SAM/BAM and FASTA/TwoBit.
Functions to remove duplications.
Functions to remove duplications.
Provides algorithms for calculating simple depth of coverage.
Provides algorithms for calculating simple depth of coverage.
Alpha - subject to change. Generator of a FASTA sequence dictionary file.
Alpha - subject to change. Generator of a FASTA sequence dictionary file.
Level analyzer of alignments in BAM.
Level analyzer of alignments in BAM.
Functions to normalize the SAM/BAM format.
Functions to normalize the SAM/BAM format.
Functions to calculate pileup from the BAM.
Functions to calculate pileup from the BAM.
Sorter of the SAM/BAM format alignments.
Sorter of the SAM/BAM format alignments.
Parser for a BAM index file.
Parser for a BAM index file.
The core of BAM index features.
The core of BAM index features.
The core of BAM features.
The core of BAM features.
Decoder of BAM alignment blocks.
Decoder of BAM alignment blocks.
Encoder of BAM alignment blocks.
Encoder of BAM alignment blocks.
Writer of BAM file format.
Writer of BAM file format.
Functions to read and write the BED (Browser Extensible Data) format. See http://genome.ucsc.edu/FAQ/FAQformat#format1 for the detail BED specifications.
Functions to read and write the BED (Browser Extensible Data) format. See http://genome.ucsc.edu/FAQ/FAQformat#format1 for the detail BED specifications.
Functions to read the bigWig format. See https://genome.ucsc.edu/goldenpath/help/bigWig.html and https://github.com/ucscGenomeBrowser/kent for the detail bigWig specifications.
Functions to read the bigWig format. See https://genome.ucsc.edu/goldenpath/help/bigWig.html and https://github.com/ucscGenomeBrowser/kent for the detail bigWig specifications.
Basic I/O of CSI:Coordinate Sorted Index files.
Basic I/O of CSI:Coordinate Sorted Index files.
The core of dictionary features.
The core of dictionary features.
Makes a sequence dictionary from FASTA data, and writes it to a file.
Makes a sequence dictionary from FASTA data, and writes it to a file.
The core of FASTA index features.
The core of FASTA index features.
Writing features for a FASTA index file.
Writing features for a FASTA index file.
Functions to read and write the FASTQ format.
Functions to read and write the FASTQ format.
Protocols of reader/writer for various file formats.
Protocols of reader/writer for various file formats.
Functions to read and write the SAM (Sequence Alignment/Map) format and BAM (its binary equivalent). See https://samtools.github.io/hts-specs/ for the detail SAM/BAM specifications.
Functions to read and write the SAM (Sequence Alignment/Map) format and BAM (its binary equivalent). See https://samtools.github.io/hts-specs/ for the detail SAM/BAM specifications.
Utilities related to SAM/BAM format.
Utilities related to SAM/BAM format.
Parser of CIGAR strings.
Parser of CIGAR strings.
Utility functions for SAM flags.
Utility functions for SAM flags.
Utility functions for SAM header.
Utility functions for SAM header.
Utility functions for SAM optional fields.
Utility functions for SAM optional fields.
Utility functions for phred quality strings.
Utility functions for phred quality strings.
Utility functions for SAM references.
Utility functions for SAM references.
Utility functions for base sequences.
Utility functions for base sequences.
Functions to read and write formats representing sequences such as FASTA and TwoBit.
Functions to read and write formats representing sequences such as FASTA and TwoBit.
Alpha - subject to change. Reader of a TABIX format file.
Alpha - subject to change. Reader of a TABIX format file.
I/O utilities.
I/O utilities.
Reading/writing functions of stream and buffer for little-endian data.
Reading/writing functions of stream and buffer for little-endian data.
Functions to read and write the VCF (Variant Call Format) format and BCF (its binary equivalent). See https://samtools.github.io/hts-specs/ for the detail VCF/BCF specifications.
Functions to read and write the VCF (Variant Call Format) format and BCF (its binary equivalent). See https://samtools.github.io/hts-specs/ for the detail VCF/BCF specifications.
A type of VCF reader and internal functions to read VCF contents. See https://samtools.github.io/hts-specs/ for the detail VCF specifications.
A type of VCF reader and internal functions to read VCF contents. See https://samtools.github.io/hts-specs/ for the detail VCF specifications.
A type of VCF writer and internal functions to write VCF contents. See https://samtools.github.io/hts-specs/ for the detail VCF specifications.
A type of VCF writer and internal functions to write VCF contents. See https://samtools.github.io/hts-specs/ for the detail VCF specifications.
Functions to read and write the WIG (Wiggle) format. See https://genome.ucsc.edu/goldenpath/help/wiggle.html for the detail WIG specifications.
Functions to read and write the WIG (Wiggle) format. See https://genome.ucsc.edu/goldenpath/help/wiggle.html for the detail WIG specifications.
Implementations of the command-line tool.
Implementations of the command-line tool.
The entry point of the command-line tool.
The entry point of the command-line tool.
General utilities.
General utilities.
Utilities for handling chromosome name.
Utilities for handling chromosome name.
Utility functions for manipulating chromosomal regions.
Utility functions for manipulating chromosomal regions.
Utilities for conversions between chromosomal positions and whole-genome positions.
Utilities for conversions between chromosomal positions and whole-genome positions.
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