Index of types

alignment [Biocaml_sam_deprecated]
High-level representation of a parsed alignment.
alignment [Biocaml_sam]
For cigar and qual, empty list indicates no value, i.e.
alignment [Biocaml_bam_alt]

background [Biocaml_pwm]
Probability distribution over an alphabet
bed_graph_value [Biocaml_wig]

cigar_op [Biocaml_sam_deprecated]
CIGAR operations.
cigar_op [Biocaml_sam]
CIGAR operations.
collection [Biocaml_jaspar]
The possible kinds of motifs.
comment [Biocaml_wig]
confusion_matrix [Biocaml_bin_pred]
content [Biocaml_track]
The "content" lines of the files.
count_matrix [Biocaml_pwm]
Type to represent gap-free alignments.
counter [Biocaml_accu]
The type of accumulators that count values

database [Biocaml_entrez]
Represents available databases

esearch_answer [Biocaml_entrez]
Represents the result of a request to esearch

fetched [Biocaml_entrez.Fetch]
fixed_step [Biocaml_wig]
fmt [Biocaml_fasta]

header [Biocaml_sam]
- sort_order: Guaranteed to be None if version = None.
header [Biocaml_fasta]
A header is a list of comment lines.
header_item [Biocaml_sam]
header_item_tag [Biocaml_sam]
Header item tags define the different types of header lines.
header_line [Biocaml_sam]

idata [Biocaml_cel]
in_channel [Biocaml_bgzf]
Representation of files opened for reading.
int_vec [Biocaml_mzData]
Vectors of OCaml ints.
irow [Biocaml_cel]
Represents row in intensity section
item [Biocaml_sam_deprecated]
High-level representation of a parsed entity.
item [Biocaml_wig]
The most general type that the default parser outputs.
item [Biocaml_vcf]
item [Biocaml_table.Row]
Type row elements (or “cells”).
item [Biocaml_psl]
item [Biocaml_lines]
item [Biocaml_gff]
The items being output by the parser.
item [Biocaml_fastq]
item [Biocaml_fasta]
item [Biocaml_bed]
The type of BED data stream items.
item0 [Biocaml_fasta]
An item0 is more raw than item.
item_to_raw [Biocaml_sam_deprecated.Error]
The error that may happen while downgrading the higher-level represtation of an alignment.
item_to_raw [Biocaml_bam.Error]
Inconsistency errors that may happen while trnasforming a Sam.item to a raw_item.
item_type [Biocaml_table.Row]
Definition of the type of a cell.

line_parsing [Biocaml_table.Row.Error]
location [Biocaml_genomeMap.Make]

motif [Biocaml_jaspar]
A Jaspar motif

offset [Biocaml_phred_score]
optional_content [Biocaml_sam_deprecated]
Alignment optional content.
optional_content_parsing [Biocaml_sam_deprecated.Error]
Errors which can happen while parsing optional content.
optional_content_value [Biocaml_sam_deprecated]
Meta-value used to store “optional content”.
optional_field [Biocaml_sam]
optional_field_value [Biocaml_sam]
The constructor encodes the TYPE and each carries its corresponding VALUE.
out_channel [Biocaml_bgzf]
Representation of files opened for writing.

parse [Biocaml_sam_deprecated.Error]
All possible parsing errors.
parse_cigar [Biocaml_bam.Error]
The potential failures while parsing the so-called CIGAR operations
parse_optional [Biocaml_bam.Error]
The potential failures while parsing the optional content in BAM alignments.
parsing [Biocaml_wig.Error]
The parsing errors.
parsing [Biocaml_track.Error]
The parsing errors that can happen while parsing Track-specific content.
parsing [Biocaml_gff.Error]
The possible parsing errors.
parsing [Biocaml_bed.Error]
The parsing errors.
parsing_base [Biocaml_bed.Error]
The parsing errors.
parsing_spec [Biocaml_bed]
The specification of how to parse the remaining columns.
platform [Biocaml_sam]
probe [Biocaml_bpmap]
program [Biocaml_sam]

range [Biocaml_rSet]
range [Biocaml_genomeMap.Make]
raw_alignment [Biocaml_sam_deprecated]
The contents of an alignment line.
raw_alignment [Biocaml_bam]
The type of an alignment record in a BAM file.
raw_bam [Biocaml_bam.Error]
The possible non-gzip-related errors encountered while parsing a BAM file.
raw_item [Biocaml_sam_deprecated]
The "items" of a parsed SAM file stream.
raw_item [Biocaml_bam]
The different kinds of items one can get from parsing a BAM file.
raw_to_item [Biocaml_sam_deprecated.Error]
The possible errors one can get while lifting SAM raw_items to higher-level representations.
raw_to_item [Biocaml_bam.Error]
All the possible errors one can encounter while going from raw_items to Sam.items.
read_group [Biocaml_sam]
record [Biocaml_gff]
The type of the GFF records/rows.
ref_seq [Biocaml_sam]
reference_sequence [Biocaml_sam_deprecated]
Definition of a reference sequence.
relation [Biocaml_accu]
rnext [Biocaml_sam]
row [Biocaml_bpmap]
Type of information on one data row.

sb_algebraic_rule [Biocaml_sbml]
sb_compartment [Biocaml_sbml]
sb_delay [Biocaml_sbml]
sb_event [Biocaml_sbml]
sb_event_assignment [Biocaml_sbml]
sb_function_definition [Biocaml_sbml]
sb_generic_rule [Biocaml_sbml]
sb_initial_assignment [Biocaml_sbml]
sb_kinetic_law [Biocaml_sbml]
sb_math [Biocaml_sbml]
sb_math_container [Biocaml_sbml]
sb_math_operator [Biocaml_sbml]
sb_model [Biocaml_sbml]
sb_parameter [Biocaml_sbml]
sb_reaction [Biocaml_sbml]
sb_rule [Biocaml_sbml]
sb_species [Biocaml_sbml]
sb_species_ref [Biocaml_sbml]
sb_trigger [Biocaml_sbml]
sb_unit [Biocaml_sbml]
sb_unit_definition [Biocaml_sbml]
section [Biocaml_bar]
sequence_id [Biocaml_fastq.Illumina]
Content of name lines as generated by Casava versions >= 1.8.
sort_order [Biocaml_sam]
spectrum [Biocaml_mzData]
Individual mass spectrum.
string_to_raw [Biocaml_sam_deprecated.Error]
The possible errors one can get while parsing SAM files.
surface [Biocaml_fastq.Illumina]

t [Biocaml_sam_deprecated.Error]
The union of all possible errors.
t [Biocaml_sam_deprecated.Flags]
Flags are represented as “bit map”.
t [Biocaml_iset]
t [Biocaml_zip.Error]
The union of the errors.
t [Biocaml_wig.Tags]
Additional tags (c.f.
t [Biocaml_wig.Error]
The union of all errors.
t [Biocaml_transform]
Type of a buffered transform converting 'inputs to 'outputs.
t [Biocaml_track.Error]
The union of all the errors.
t [Biocaml_track]
The type of the parser "track" lines.
t [Biocaml_table.Row.Error]
t [Biocaml_table.Row.Tags]
The tags associated with table rows: `separator c adds c in the list of separators used., `strict_about something ensures that the format is fully compliant with something (example: otherwise the parser may ignore some errors to keep going). , `tail_format array describes the format of the columns of the row, if not provided everything is assumed to be `type_string.
t [Biocaml_table.Row]
A single row.
t [Biocaml_strand]
Only valid values are '-' or '+'.
t [Biocaml_solexa_score]
t [Biocaml_sgr]
t [Biocaml_seq_range.Make]
t [Biocaml_seq]
Type of a sequence
t [Biocaml_sam.Flags]
Flags are represented as a "bit map".
t [Biocaml_rSet]
Type of a set of integers.
t [Biocaml_roman_num]
t [Biocaml_range]
Type of a range.
t [Biocaml_pwm]
Representation of a PWM
t [Biocaml_psl.Error]
t [Biocaml_pos]
t [Biocaml_phred_score]
t [Biocaml_msg.Tree]
t [Biocaml_mzData.Precursor]
t [Biocaml_lines.Buffer]
The buffer handle.
t [Biocaml_line]
A line is simply a string, possibly empty, that does not contain a newline character.
t [Biocaml_interval_tree]
t [Biocaml_histogram]
The type of a histogram whose bin limits are of type 'a.
t [Biocaml_gff.Tags]
Additional format-information tags (c.f.
t [Biocaml_gff.Error]
The union of all the errors of this module.
t [Biocaml_genomeMap.Chromosome]
t [Biocaml_genomeMap.Make.Signal]
t [Biocaml_genomeMap.Make.LMap]
t [Biocaml_genomeMap.Make.LSet]
t [Biocaml_genomeMap.Make.Selection]
t [Biocaml_entrez.Make.Gene]
t [Biocaml_entrez.Make.Pubmed]
t [Biocaml_entrez.Make.PubmedSummary]
t [Biocaml_entrez.Make.Gene_ref]
t [Biocaml_entrez.Make.Dbtag]
t [Biocaml_entrez.Make.Object_id]
t [Biocaml_chr.Error]
Possible errors:
t [Biocaml_cel]
The type of a CEL file.
t [Biocaml_bpmap]
Type of a BPMAP file.
t [Biocaml_bed.Error]
The union of all the errors.
t [Biocaml_bar]
Type of a BAR file, which can be thought of as a header plus set of sections.
t [Biocaml_bam_alt.Alignment0]
t [Biocaml_bam_alt.Header]
t [Biocaml_bam.Error]
The union of all the errors.
t [Biocaml_accu.Relation]
t [Biocaml_accu.Counter]
t [Biocaml_accu]
General type for accumulators: 'instances are mapped to 'bins, and the 'accumulated value for a 'bin is updated with an 'increment
t_type [Biocaml_table.Row]
Definition of the type of a row.
tag_value [Biocaml_sam]
A tag-value pair comprising the content of header items.
tile [Biocaml_fastq.Illumina]
to_bed_graph [Biocaml_wig.Error]
The errors encountered while transforming item values to bed-graph-only values.

unzip [Biocaml_zip.Error]
The possible unzipping errors.

variable_step [Biocaml_wig]
vcf_alt_meta [Biocaml_vcf]
vcf_description [Biocaml_vcf]
vcf_filter_meta [Biocaml_vcf]
vcf_format [Biocaml_vcf]
vcf_format_meta [Biocaml_vcf]
vcf_format_type [Biocaml_vcf]
Types, allowed for VCF FORMAT meta header.
vcf_id [Biocaml_vcf]
vcf_info [Biocaml_vcf]
vcf_info_meta [Biocaml_vcf]
vcf_info_type [Biocaml_vcf]
Types, allowed for VCF INFO meta header.
vcf_meta [Biocaml_vcf]
vcf_number [Biocaml_vcf]
vcf_parse_error [Biocaml_vcf]
vcf_parse_row_error [Biocaml_vcf]
vcf_row [Biocaml_vcf]
vec [Biocaml_mzData]
Vectors of 64 bits floats.