Biocaml 0.4-dev

biocaml.org

All modules are named with a Biocaml_ prefix to avoid name clashes with other libraries. For convenience, every module Biocaml_foo is renamed as Foo under the main Biocaml module. Thus, do open Biocaml in your code to use the shorter names.

Files


Biocaml_bam
Parsing and printing of BAM files.
Biocaml_bar
Affymetrix's BAR files.
Biocaml_bed
BED data files.
Biocaml_bpmap
Affymetrix's BPMAP files.
Biocaml_cel
Affymetrix's CEL files.
Biocaml_fasta
FASTA files.
Biocaml_fastq
FASTQ data.
Biocaml_gff
GFF files.
Biocaml_jaspar
Access to Jaspar database
Biocaml_lines
Manipulate the lines of a file.
Biocaml_mzData
Read mzData files (mass spectrometry data format).
Biocaml_psl
PSL files.
Biocaml_sam
SAM files.
Biocaml_sgr
Sequence Graph (SGR) files.
Biocaml_track
Track files in UCSC Genome Browser format.
Biocaml_wig
WIG data.
Biocaml_zip
Streaming interface to the Zlib library.

Tags classify file types.
Biocaml_tags
Meta-information about files and their formats.

Internet


Biocaml_entrez
Entrez Utilities API

Data Structures


Biocaml_accu
A datastructure (based on Hashtbl) to accumulate values.
Biocaml_genomeMap
Data structures to represent sets of (possibly annotated) genomic regions
Biocaml_histogram
Histograms with polymorphic bin types.
Biocaml_interval_tree
Interval tree (data structure)
Biocaml_range
Ranges of contiguous integers (integer intervals).
Biocaml_rSet
Efficient integer sets when many elements expected to be large contiguous sequences of integers.
Biocaml_table
Generic “tables” (like CSV, TSV, Bed …).

Analysis


Biocaml_bin_pred
Performance measurement of binary classifiers.
Biocaml_math
Numeric mathematics.
Biocaml_pwm
Position-weight matrix

Strings


Biocaml_chr
Chromosome names.
Biocaml_line
Single line of text.
Biocaml_strandName
Strand names.

Utilities


Biocaml_about
General information about this library.
Biocaml_msg
Consistent printing of errors, warnings, and bugs.
Biocaml_pos
File positions.
Biocaml_phred_score
PHRED quality scores.
Biocaml_romanNum
Roman numerals.
Biocaml_solexa_score
Solexa quality scores.
Biocaml_transform
Buffered transforms.

Incubator


Biocaml_sbml
SBML file parser.
Biocaml_seq
Nucleic acid sequences.

Internal


Biocaml_internal_utils
Internal utility functions that are commonly needed in many places.

Documentation generated on: Wed Jul 16 22:23:18 UTC 2014

Git commit: a9d8fb02579126c47b4ed9376db258e8bee314ec