Spec BamFileIn
Class for reading SAM and BAM files.

Extends FormattedFileIn
All Extended FormattedFile, FormattedFileIn
Defined in <seqan/bam_io.h>
Signature typedef FormattedFile<Bam, Input> BamFileIn;

Member Function Overview

Member Functions Inherited From FormattedFile

Interface Function Overview

Interface Functions Inherited From FormattedFile

Interface Functions Inherited From FormattedFileIn

Interface Metafunction Overview

Interface Metafunctions Inherited From FormattedFile

Detailed Description

Example

Access SAM or BAM files.

#include <seqan/bam_io.h>

using namespace seqan;

int main()
{
    CharString bamFileName = getAbsolutePath("demos/tutorial/sam_and_bam_io/example.sam");

    // Open input file, BamFileIn can read SAM and BAM files.
    BamFileIn bamFileIn;
    if (!open(bamFileIn, toCString(bamFileName)))
    {
        std::cerr << "ERROR: Could not open " << bamFileName << std::endl;
        return 1;
    }
    // Open output file, BamFileOut accepts also an ostream and a format tag.
    BamFileOut bamFileOut(context(bamFileIn), std::cout, Sam());

    try
    {
        // Copy header.
        BamHeader header;
        readHeader(header, bamFileIn);
        writeHeader(bamFileOut, header);

        // Copy records.
        BamAlignmentRecord record;
        while (!atEnd(bamFileIn))
        {
            readRecord(record, bamFileIn);
            writeRecord(bamFileOut, record);
        }
    }
    catch (Exception const & e)
    {
        std::cout << "ERROR: " << e.what() << std::endl;
        return 1;
    }

    return 0;
}
Demo: demos/tutorial/sam_and_bam_io/solution1.cpp

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	*

See Also

Interface Functions Detail

bool jumpToOrphans(bamFileIn, hasAlignments, index);

Seek to orphans block in BamFileIn using an index.

Parameters

bamFileIn The BamFileIn object to jump with.
hasAlignments A bool that is set to true if there are any orphans.
index The BamIndex to use for jumping.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

bool jumpToRegion(bamFileIn, hasAlignments, refID, regionStart, regionEnd, index);

Seek in BamFileIn using an index.

Parameters

bamFileIn The BamFileIn to jump with.
hasAlignments A bool that is set true if the region [regionStart, regionEnd] has any at least one overlapping alignment (bam record).
refID The reference id to jump to (int32_t).
regionStart The begin of the region to jump to (int32_t).
regionEnd The end of the region to jump to (int32_t).
index The BamIndex to use for the jumping.

Returns

bool true if seeking was successful, false if not.

You provide a region [regionStart, regionEnd] on the reference refID that you want to jump to and the function jumps to the first alignment (bam record) whose start position lies inside this region, if any. Note: The current inmplementation only consideres the read start positions. Therefore, we do guarantee that reads overlapping the region are included. To account for this limitation you may want to choose the start of your your region with an appropiate offset (e.g. start - length_of_read).

Remarks

This function fails if refID/regionStart are invalid.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.