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cljam.algo.bam-indexer

Indexer of BAM.

Indexer of BAM.
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cljam.algo.convert

Converters between equivalent formats: SAM/BAM and FASTA/TwoBit.

Converters between equivalent formats: SAM/BAM and FASTA/TwoBit.
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cljam.algo.dedupe

Functions to remove duplications.

Functions to remove duplications.
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cljam.algo.depth

Provides algorithms for calculating simple depth of coverage.

Provides algorithms for calculating simple depth of coverage.
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cljam.algo.dict

Alpha - subject to change. Generator of a FASTA sequence dictionary file.

Alpha - subject to change.
Generator of a FASTA sequence dictionary file.
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cljam.algo.fasta-indexer

Indexer of FASTA.

Indexer of FASTA.
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cljam.algo.level

Level analyzer of alignments in BAM.

Level analyzer of alignments in BAM.
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cljam.algo.normal

Functions to normalize the SAM/BAM format.

Functions to normalize the SAM/BAM format.
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cljam.algo.sorter

Sorter of the SAM/BAM format alignments.

Sorter of the SAM/BAM format alignments.
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cljam.algo.vcf-indexer

Indexer of VCF/BCF.

Indexer of VCF/BCF.
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cljam.io.bam-index

Parser for a BAM index file.

Parser for a BAM index file.
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cljam.io.bam.core

The core of BAM features.

The core of BAM features.
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cljam.io.bam.encoder

Encoder of BAM alignment blocks.

Encoder of BAM alignment blocks.
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cljam.io.bam.reader

Reader of BAM file format.

Reader of BAM file format.
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cljam.io.bed

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.
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cljam.io.bigwig

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.
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cljam.io.csi

Basic I/O of CSI:Coordinate Sorted Index files.

Basic I/O of CSI:Coordinate Sorted Index files.
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cljam.io.dict.core

The core of dictionary features.

The core of dictionary features.
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cljam.io.dict.writer

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.
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cljam.io.fasta-index.core

The core of FASTA index features.

The core of FASTA index features.
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cljam.io.fasta-index.reader

Reading FASTA index file

Reading FASTA index file
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cljam.io.fasta-index.writer

Writing features for a FASTA index file.

Writing features for a FASTA index file.
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cljam.io.sam

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.
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cljam.io.sam.util.refs

Utility functions for SAM references.

Utility functions for SAM references.
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cljam.io.sam.util.sequence

Utility functions for base sequences.

Utility functions for base sequences.
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cljam.io.sam.writer

Provides writing features.

Provides writing features.
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cljam.io.sequence

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.
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cljam.io.tabix

Alpha - subject to change. Reader of a TABIX format file.

Alpha - subject to change.
Reader of a TABIX format file.
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cljam.io.util.lsb

Reading/writing functions of stream and buffer for little-endian data.

Reading/writing functions of stream and buffer for little-endian data.
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cljam.io.vcf

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.
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cljam.io.vcf.reader

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.
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cljam.io.vcf.writer

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.
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cljam.io.wig

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.
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cljam.tools.cli

Implementations of the command-line tool.

Implementations of the command-line tool.
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cljam.tools.main

The entry point of the command-line tool.

The entry point of the command-line tool.
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cljam.util.whole-genome

Utilities for conversions between chromosomal positions and whole-genome positions.

Utilities for conversions between chromosomal positions and whole-genome
positions.
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