A | |
alignment [Biocaml_sam] |
High-level representation of a parsed alignment.
|
B | |
background [Biocaml_pwm] |
Probability distribution over an alphabet
|
bed_graph_value [Biocaml_wig] | |
C | |
char_seq [Biocaml_fasta] |
A sequence of characters.
|
cigar_op [Biocaml_sam] |
CIGAR operations.
|
collection [Biocaml_jaspar] |
The possible kinds of motifs.
|
comment [Biocaml_wig] | |
confusion_matrix [Biocaml_roc] | |
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 | |
fasta_pair_to_fastq [Biocaml_fastq.Error] |
The errors of the
Biocaml_fastq.Transform.fasta_pair_to_fastq .
|
fetched [Biocaml_entrez.Fetch] | |
file_format [Biocaml_tags] |
Description of file formats.
|
fixed_step [Biocaml_wig] | |
I | |
idata [Biocaml_cel] | |
input_error [Biocaml_tags.Input_transform] |
An union of all possible input errors.
|
int_seq [Biocaml_fasta] |
A sequence of integer quality scores.
|
int_vec [Biocaml_mzData] |
Vectors of OCaml ints.
|
irow [Biocaml_cel] |
Represents row in intensity section
|
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_sam] |
High-level representation of a parsed entity.
|
item [Biocaml_psl] | |
item [Biocaml_lines] | Lines.item is a Line.t
|
item [Biocaml_gff] |
The items being output by the parser.
|
item [Biocaml_fastq] |
Type of FASTQ items.
|
item [Biocaml_fasta] |
A named FASTA item.
|
item [Biocaml_bed] |
The type of BED data stream items.
|
item_to_raw [Biocaml_sam.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] | |
M | |
motif [Biocaml_jaspar] |
The main “Jaspar element”.
|
O | |
optional_content [Biocaml_sam] |
Alignment optional content.
|
optional_content_parsing [Biocaml_sam.Error] |
Errors which can happen while parsing optional content.
|
optional_content_value [Biocaml_sam] |
Meta-value used to store “optional content”.
|
output_error [Biocaml_tags.Output_transform] |
Union possible output errors of the transforms
leading to
Biocaml_sam.item values.
|
P | |
parse [Biocaml_sam.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_fastq.Error] |
The 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.
|
probe [Biocaml_bpmap] | |
R | |
range [Biocaml_rSet] | |
range [Biocaml_genomeMap] | |
raw_alignment [Biocaml_sam] |
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] |
The "items" of a parsed SAM file stream.
|
raw_item [Biocaml_fasta] |
Lowest level items parsed by this module:
|
raw_item [Biocaml_bam] |
The different kinds of items one can get from parsing a BAM file.
|
raw_to_item [Biocaml_sam.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.
|
record [Biocaml_gff] |
The type of the GFF records/rows.
|
reference_sequence [Biocaml_sam] |
Definition of a reference sequence.
|
relation [Biocaml_accu] | |
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] | |
specification [Biocaml_fasta.Random] |
The specification guiding the random generation of
'a raw_item
values is a list of specification values.
|
spectrum [Biocaml_mzData] |
Individual mass spectrum.
|
string_to_raw [Biocaml_sam.Error] |
The possible errors one can get while parsing SAM files.
|
string_to_raw_item [Biocaml_fasta.Error] |
Errors raised when converting a string to a
Biocaml_fasta.raw_item .
|
T | |
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_tags.Input_transform] |
The general input transformation.
|
t [Biocaml_tags.Output_transform] |
Generic union of possible output transforms.
|
t [Biocaml_tags] |
Description of multiple file formats.
|
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_strandName] |
Type of strand.
|
t [Biocaml_solexa_score] | |
t [Biocaml_sgr] | |
t [Biocaml_seq] |
Type of a sequence
|
t [Biocaml_sam.Error] |
The union of all possible errors.
|
t [Biocaml_sam.Flags] |
Flags are represented as “bit map”.
|
t [Biocaml_rSet] |
Type of a set of integers.
|
t [Biocaml_romanNum] |
Type of a roman numeral.
|
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_lines.Error] |
Errors:
`premature_end_of_input - expected more lines than available.
|
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.LMap_spec] | |
t [Biocaml_genomeMap.Signal] | |
t [Biocaml_genomeMap.LMap] | |
t [Biocaml_genomeMap.LSet] | |
t [Biocaml_genomeMap.Selection] | |
t [Biocaml_fastq.Error] |
Union of all possible errors.
|
t [Biocaml_fasta.Error] |
Union of all errors.
|
t [Biocaml_fasta.Tags] |
The format details for any kind of FASTA file.
|
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.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.
|
tags [Biocaml_tags.Input_transform] |
An alias of the type
Tags.t .
|
tags [Biocaml_tags.Output_transform] |
Alias to
Tags.t for this module.
|
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.
|