Class
GenomicRegionStore information about a genomic region.
Defined in | <seqan/seq_io.h> |
---|---|
Signature |
class GenomicRegion;
|
Member Function Overview
Interface Function Overview
-
void clear(genomicRegion);
Reset a GenomicRegion object to the same state after default construction. -
bool parse(genomicRegion, regionString);
Parse genomic region string store results in GenomicRegion.
Member Variable Overview
-
__int32 GenomicRegion::beginPos
Begin position of the range on the chromosome. Default is -1. -
__int32 GenomicRegion::endPos
End position of the range on the chromosome. Default is -1. -
__int32 GenomicRegion::seqId
An optional field storing an integer. Default is -1. -
CharString GenomicRegion::seqName
Name of the sequence the region lies on, default is the empty string.
Detailed Description
A genomic region is a range on a chromosome. The chromosome is identified by its name (as text in seqName, optionally also as an integer in seqId). The range is stored as a half-open interval [beginPos, endPos). If beginPos is set to -1 then the range spans the whole chromosome. If beginPos is set to a value >= 0 and endPos is set ot -1, then the chromosome is selected from beginPos to the end.
Examples for genomic regions are chr1, chr1:1,000, chr1:1,000-2,000.
The textual description of a genomic region has one of the formats NAME, NAME:START, NAME:START-END. The positions in the textual representation START and END are one-based. However, the representation in the members of GenomicRegion is zero-based.
Examples
Construct a GenomicRegion object and fill it from different region strings.
seqan::GenomicRegion genomicRegion; parse(genomicRegion, "chr1"); // genomicRegion.seqName == "chr1" // genomicRegion.seqId == -1, genomicRegion.beginPos == -1, genomicRegion.beginPos == -1 parse(genomicRegion, "chr1:1000"); // genomicRegion.seqName == "chr1" // genomicRegion.beginPos == 999 // genomicRegion.seqId == -1, genomicRegion.beginPos == -1 parse(genomicRegion, "chr1:1000-2000"); // genomicRegion.seqName == "chr1" // genomicRegion.beginPos == 999 // genomicRegion.beginPos == 2000 // genomicRegion.seqId == -1
Member Functions Detail
GenomicRegion::GenomicRegion();
GenomicRegion::GenomicRegion(str);
Parameters
str
|
The string to parse region from. Types: CharString |
---|
The default constructor sets all integer members to -1, the seqName member is left empty.
Interface Functions Detail
void clear(genomicRegion);
Parameters
genomicRegion
|
The GenomicRegion object to reset. Types: GenomicRegion |
---|
bool parse(genomicRegion, regionString);
Parameters
regionString
|
The region string to prse. Types: CharString. |
---|---|
genomicRegion
|
The GenomicRegion object to write the results to. Types: GenomicRegion |
Returns
bool |
true indicates successful parsing. |
---|