Index of types

A
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]
B
background [Biocaml_pwm]	Probability distribution over an alphabet
bed_graph_value [Biocaml_wig]
C
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
D
database [Biocaml_entrez]	Represents available databases
E
esearch_answer [Biocaml_entrez]	Represents the result of a request to esearch
F
fetched [Biocaml_entrez.Fetch]
fixed_step [Biocaml_wig]
fmt [Biocaml_fasta]
H
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]	@HD.
I
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.
L
line_parsing [Biocaml_table.Row.Error]
location [Biocaml_genomeMap.Make]
M
motif [Biocaml_jaspar]	A Jaspar motif
O
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.
P
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]	@PG.
R
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_item`s to `Sam.item`s.
read_group [Biocaml_sam]	@RG.
record [Biocaml_gff]	The type of the GFF records/rows.
ref_seq [Biocaml_sam]	@SQ.
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.
S
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
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 `'input`s to `'output`s.
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: `'instance`s are mapped to `'bin`s, and the `'accu`mulated 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.
U
unzip [Biocaml_zip.Error]	The possible unzipping errors.
V
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.