| 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. GenomicRegion Include Headers seqan/seq_io.h Data Members
beginPos | Begin position of the range on the chromosome. Default is -1.
endPos | End position of the range on the chromosome. Default is -1.
seqId | An optional field storing an integer. Default is -1.
seqName | Name of the sequence the region lies on, default is the empty string.
Member Functions
GenomicRegion | Constructor.
Functions
clear | Reset a GenomicRegion object to the same state after default construction.
parse | Parse genomic region string store results in GenomicRegion.
readRegion | Load the infix of a sequence from a FaiIndex.
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 SeqAn - Sequence Analysis Library - www.seqan.de

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