module Accu : sig ... endA datastructure (based on Hashtbl) to accumulate values.
module Bam : sig ... endRead and write BAM format.
module Bamstats : sig ... endmodule Bar : sig ... endAffymetrix's BAR files. Their Tiling Analysis Software (TAS) produces BAR files in binary format but this module supports only the text format generated by selecting the "Export probe analysis as TXT" option.
module Bed : sig ... endBED data files.
module Bgzf : sig ... endI/O on Blocked GNU Zip format (BGZF) files
module Bin_pred : sig ... endPerformance measurement of binary classifiers.
module Biocaml_result : sig ... endExtension of Core's Result. Internal use only.
module Bpmap : sig ... endAffymetrix's BPMAP files. Only text format supported. Binary BPMAP files must first be converted to text using Affymetrix's probe exporter tool.
module Cel : sig ... endAffymetrix's CEL files. Only text format supported. Binary file must be converted using Affymetrix's conversion tool. This tool does not change file extension, so be sure your file really is in text format.
module Chr : sig ... endChromosome names. A chromosome name, as defined by this module, consists of two parts. An optional prefix "chr" (case-insensitive), followed by a suffix identifying the chromosome. The possible suffixes (case-insensitive) are:
module Entrez : sig ... endEntrez Utilities API
module Fasta : sig ... endmodule Fastq : sig ... endFASTQ files. The FASTQ file format is repeated sequence of 4 lines:
module File_mapper : sig ... endmodule Future : sig ... endmodule Future_unix : sig ... endmodule GenomeMap : sig ... endData structures to represent sets of (possibly annotated) genomic regions
module Gff : sig ... endGFF files.
module Histogram : sig ... endHistograms with polymorphic bin types.
module Interval_tree : sig ... endInterval tree (data structure)
module Iset : sig ... endDIET : Discrete Interval Encoding Trees
module Jaspar : sig ... endAccess to Jaspar database
module Line : sig ... endmodule Lines : sig ... endManipulate the lines of a file.
module Math : sig ... endNumeric mathematics.
module Msg : sig ... endConsistent printing of errors, warnings, and bugs. An error is a user mistake that prevents continuing program execution, a warning is a milder problem that the program continues to execute through, and a bug is a mistake in the software.
module MzData : sig ... endmodule Phred_score : sig ... endPHRED quality scores.
module Pos : sig ... endFile positions. A position within a file is defined by:
module Psl : sig ... endmodule Pwm : sig ... endPosition-weight matrix
module RSet : sig ... endEfficient integer sets when many elements expected to be large contiguous sequences of integers.
module Range : sig ... endRanges of contiguous integers (integer intervals). A range is a contiguous sequence of integers from a lower bound to an upper bound. For example, [2, 10] is the set of integers from 2 through 10, inclusive of 2 and 10.
module Roman_num : sig ... endRoman numerals. Values greater than or equal to 1 are valid roman numerals.
module Sam : sig ... endSAM files. Documentation here assumes familiarity with the SAM specification.
module Sbml : sig ... endSBML file parser. Currently only level 2 version 4 is supported.
module Seq : sig ... endNucleic acid sequences. A nucleic acid code is any of A, C, G, T, U, R, Y, K, M, S, W, B, D, H, V, N, or X. See IUB/IUPAC standards for further information. Gaps are not supported. Internal representation uses uppercase, but constructors are case-insensitive. By convention the first nucleic acid in a sequence is numbered 1.
module Seq_range : sig ... endRange on a sequence, where the sequence is represented by an identifier.
module Sgr : sig ... endSequence Graph (SGR) files.
module Solexa_score : sig ... endSolexa quality scores.
module Strand : sig ... endStrand names. There are various conventions for referring to the two strands of DNA. This module provides an of_string function that parses the various conventions into a canonical representation, which we define to be '-' or '+'.
module Table : sig ... endGeneric “tables” (like CSV, TSV, Bed …).
module Tfxm : sig ... endBuffered transforms. A buffered transform represents a method for converting a stream of inputs to a stream of outputs. However, inputs can also be buffered, i.e. you can feed inputs to the transform and pull out outputs later. There is no requirement that 1 input produces exactly 1 output. It is common that multiple input values are needed to construct a single output, and vice versa.
module Track : sig ... endTrack files in UCSC Genome Browser format. The following documentation assumes knowledge of concepts explained on the UCSC Genome Browser's website. Basically, a track file is one of several types of data (WIG, GFF, etc.), possibly preceded by comments, browser lines, and a track line. This module allows only a single data track within a file, although the UCSC specifies that multiple tracks may be provided together.
module Transcripts : sig ... endTranscripts are integer intervals containing a list of exons. Exons are themselves defined as a list of integer intervals.
module Vcf : sig ... endParsing of VCF files.
module Wig : sig ... endWIG data.
module Zip : sig ... endStreaming interface to the Zlib library.