BamStream

Class

BamStream

Class that provides an easy to use interface for reading and writing SAM and BAM files.

BamStream

Include Headers

seqan/bam_io.h

Data Members

bamIOContext	The BamIOContext object to use for reading and writing BamAlignmentRecords.
header	The BamHeader of the BamStream object.

Member Functions

BamStream

Constructor

Functions

atEnd	Check whether a BamStream object is at end when reading.
close	Close BamStream object's underlying file.
flush	Flush output when writing.
isGood	Check whether the BamStream object has is in the failure state.
open	Open a BamStream object for reading/writing.
readRecord	Read one BamAlignmentRecord from a BamStream.
reset	Reset BamStream object to status after construction.
writeRecord	Write one BamAlignmentRecord to a BamStream.

Examples

Read and write SAM or BAM files.

File "bam_stream.cpp"

1	#include <iostream>
2	#include <seqan/file.h>
3	#include <seqan/bam_io.h>
4
5	using namespace seqan;
6
7	int main()
8	{
9	// Open input stream, BamStream can read SAM and BAM files.
10	std::string pathSam = std::string(SEQAN_PATH_TO_ROOT()) + "/core/demos/bam_io/example.sam";
11
12	BamStream bamStreamIn(pathSam.c_str());
13	if (!isGood(bamStreamIn))
14	{
15	std::cerr << "Can't open the file." << std::endl;
16	return 1;
17	}
18
19	// Open output stream. The value "-" means reading from stdin or writing to stdout.
20	BamStream bamStreamOut("-", BamStream::WRITE);
21	// Copy header. The header is automatically written out before the first record.
22	bamStreamOut.header = bamStreamIn.header;
23
24	// BamAlignmentRecord stores one record at a time.
25	BamAlignmentRecord record;
26	while (!atEnd(bamStreamIn))
27	{
28	if (readRecord(record, bamStreamIn) != 0)
29	{
30	std::cerr << "Can't read record!" << std::endl;
31	return 1;
32	}
33	if (writeRecord(bamStreamOut, record) != 0)
34	{
35	std::cout << "Can't write record!" << std::endl;
36	return 1;
37	}
38	}
39	return 0;
40	}
41

The output is as follows:

@HD VN:1.3  SO:coordinate
@SQ SN:ref  LN:45
@SQ SN:ref2 LN:40
r001    163 ref 7   30  8M4I4M1D3M  =   37  39  TTAGATAAAGAGGATACTG *   XX:B:S,12561,2,20,112
r002    0   ref 9   30  1S2I6M1P1I1P1I4M2I  *   0   0   AAAAGATAAGGGATAAA   *
r003    0   ref 9   30  5H6M    *   0   0   AGCTAA  *
r004    0   ref 16  30  6M14N1I5M   *   0   0   ATAGCTCTCAGC    *
r003    16  ref 29  30  6H5M    *   0   0   TAGGC   *
r001    83  ref 37  30  9M  =   7   -39 CAGCGCCAT   *

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