Class Specialization
BGZF Stream
Reading and writing of BGZF data.
BGZF Stream
Include Headers
Not copy constructable, not assignable.
BGZF is the Block GZip Format which is used as the underlying format for BAM and TABIX. Data is written out compressed with gzip but the uncompressed data is split into blocks with a maximum block size. It is therefore possible to jump to beginnings of blocks in the resulting files, decompress the block and then jump into the block itself.
Specialization of
atEndDetermines whether an iterator is at the end position. (Stream)
attachToFileAttach to already open input / output file.
checkEofCheck that the EOF marker is present in a BGZF(/BAM) file.
closeCloses a file. (Stream)
jumpToOrphansSeek to orphans block in BAM BGZF stream using an index.
jumpToRegionSeek in BAM BGZF stream using an index.
openOpens a file, stream, or persistent string.
sizeGets the file size.
Stream<Bgzf> stream;
if (!open(stream, "myfile.bam", "r"))
    return 1;  // error
// ... work
SeqAn - Sequence Analysis Library -

Page built @2013/07/11 09:12:19