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Index of modules


A
About [Biocaml]
Accu [Biocaml]
Alignment0 [Biocaml_bam_alt]
Representation of partially parsed alignments.
Array [Biocaml_internal_utils]

B
Bam [Biocaml]
Bam_alt [Biocaml]
Bar [Biocaml]
Bed [Biocaml]
Bin_pred [Biocaml]
Biocaml
Biocaml_about
General information about this library.
Biocaml_accu
A datastructure (based on Hashtbl) to accumulate values.
Biocaml_bam
Parsing and printing of BAM files.
Biocaml_bam_alt
Read and write BAM format.
Biocaml_bar
Affymetrix's BAR files.
Biocaml_bed
BED data files.
Biocaml_bgzf
I/O on Blocked GNU Zip format (BGZF) files
Biocaml_bin_pred
Performance measurement of binary classifiers.
Biocaml_bpmap
Affymetrix's BPMAP files.
Biocaml_cel
Affymetrix's CEL files.
Biocaml_chr
Chromosome names.
Biocaml_entrez
Entrez Utilities API
Biocaml_fasta
FASTA files.
Biocaml_fastq
FASTQ files.
Biocaml_genomeMap
Data structures to represent sets of (possibly annotated) genomic regions
Biocaml_gff
GFF files.
Biocaml_histogram
Histograms with polymorphic bin types.
Biocaml_internal_utils
Internal utility functions that are commonly needed in many places.
Biocaml_interval_tree
Interval tree (data structure)
Biocaml_iset
DIET : Discrete Interval Encoding Trees
Biocaml_jaspar
Access to Jaspar database
Biocaml_line
Single line of text.
Biocaml_lines
Manipulate the lines of a file.
Biocaml_math
Numeric mathematics.
Biocaml_msg
Consistent printing of errors, warnings, and bugs.
Biocaml_mzData
Read mzData files (mass spectrometry data format).
Biocaml_phred_score
PHRED quality scores.
Biocaml_pos
File positions.
Biocaml_psl
PSL files.
Biocaml_pwm
Position-weight matrix
Biocaml_rSet
Efficient integer sets when many elements expected to be large contiguous sequences of integers.
Biocaml_range
Ranges of contiguous integers (integer intervals).
Biocaml_roman_num
Roman numerals.
Biocaml_sam
SAM files.
Biocaml_sam_deprecated
SAM files and SAM-alignements high-level representation.
Biocaml_sbml
SBML file parser.
Biocaml_seq
Nucleic acid sequences.
Biocaml_seq_range
Range on a sequence, where the sequence is represented by an identifier.
Biocaml_sgr
Sequence Graph (SGR) files.
Biocaml_solexa_score
Solexa quality scores.
Biocaml_strand
Strand names.
Biocaml_table
Generic "tables" (like CSV, TSV, Bed ...).
Biocaml_track
Track files in UCSC Genome Browser format.
Biocaml_transcripts
Transcripts are integer intervals containing a list of exons.
Biocaml_transform
Buffered transforms.
Biocaml_vcf
Parsing of VCF files.
Biocaml_wig
WIG data.
Biocaml_zip
Streaming interface to the Zlib library.
Bpmap [Biocaml]
Buffer [Biocaml_lines]

C
Cel [Biocaml]
Chr [Biocaml]
Counter [Biocaml_accu]

D
Dbtag [Biocaml_entrez.Make]
Debug [Biocaml_internal_utils]
Default [Biocaml_zip]

E
Entrez [Biocaml]
Error [Biocaml_sam_deprecated]
Error [Biocaml_zip]
Error [Biocaml_wig]
Error [Biocaml_track]
Error [Biocaml_table.Row]
Error [Biocaml_psl]
Error [Biocaml_gff]
Error [Biocaml_chr]
Error [Biocaml_bed]
Error [Biocaml_bam]

F
Fasta [Biocaml]
Fastq [Biocaml]
Flags [Biocaml_sam_deprecated]
Flags [Biocaml_sam]
Alignment Types

G
Gene [Biocaml_entrez.Make]
Gene_ref [Biocaml_entrez.Make]
GenomeMap [Biocaml]
Gff [Biocaml]

H
Header [Biocaml_bam_alt]
BAM header files contain a plain text SAM header, plus additional information related to the encoding of the file.
Histogram [Biocaml]

I
Illumina [Biocaml_fastq]
Illumina-specific operations
Interval_tree [Biocaml]

J
Jaspar [Biocaml]

L
LMap [Biocaml_genomeMap.Make]
A set of locations with an attached value on each of them
LSet [Biocaml_genomeMap.Make]
A set of locations (e.g.
Line [Biocaml_internal_utils]
Line [Biocaml]
Lines [Biocaml]
List [Biocaml_internal_utils.Result]

M
Make [Biocaml_seq_range]
Make [Biocaml_genomeMap]
Make [Biocaml_entrez]
MakeIO [Biocaml_sam]
Input/Output
MakeIO [Biocaml_lines]
MakeIO [Biocaml_fastq]
Input/Output
Math [Biocaml]
Msg [Biocaml]
MzData [Biocaml]

O
Object_id [Biocaml_entrez.Make]

P
Phred_score [Biocaml]
Pos [Biocaml_internal_utils]
Pos [Biocaml]
Precursor [Biocaml_mzData]
Psl [Biocaml]
Pubmed [Biocaml_entrez.Make]
PubmedSummary [Biocaml_entrez.Make]
Pwm [Biocaml]

R
RSet [Biocaml]
Range [Biocaml]
Relation [Biocaml_accu]
Result [Biocaml_internal_utils]
Roman_num [Biocaml]
Row [Biocaml_table]

S
Sam [Biocaml]
Sbml [Biocaml]
Selection [Biocaml_genomeMap.Make]
A collection of non-overlapping regions (e.g.
Seq [Biocaml]
Seq_range [Biocaml]
Sgr [Biocaml]
Solexa_score [Biocaml]
Strand [Biocaml]
Stream [Biocaml_internal_utils]

T
Table [Biocaml]
Tags [Biocaml_wig]
Tags [Biocaml_table.Row]
Tags [Biocaml_gff]
Track [Biocaml]
Transform [Biocaml_sam_deprecated]
Transform [Biocaml_zip]
Transform [Biocaml_wig]
Transform [Biocaml_vcf]
Transform [Biocaml]
Transform [Biocaml_track]
Transform [Biocaml_table.Row]
Transform [Biocaml_psl]
Transform [Biocaml_lines]
Transform [Biocaml_gff]
Transform [Biocaml_bed]
Transform [Biocaml_bam]
Tree [Biocaml_msg]
Message tree for more complex messages.

U
Url [Biocaml_internal_utils]
Operations on URL-style encodings.

V
Vcf [Biocaml]

W
Wig [Biocaml]

Z
Zip [Biocaml]

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