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.

FASTA files.

FASTQ files.

GFF files.

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

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

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_roman_num

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: Fri Dec 19 19:21:15 UTC 2014

Git commit: d9026a03e89d0ca9162df277544696a3c9579a49