Class
GenomicRegion
Store information about a genomic region.
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.
Include Headers
seqan/seq_io.h
Data Members
Begin position of the range on the chromosome. Default is | |
End position of the range on the chromosome. Default is | |
An optional field storing an integer. Default is | |
Name of the sequence the region lies on, default is the empty string. |
Member Functions
Constructor. |
Functions
Reset a GenomicRegion object to the same state after default construction. | |
Parse genomic region string store results in GenomicRegion. | |
Load the infix of a sequence from a FaiIndex. |
Examples
Construct a GenomicRegion object and fill it from different region strings.
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
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