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378 bytes added
, 08:19, 11 August 2010
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| | <code>bool SamFile::SetReadSection(int32_t refID, int32_t start, int32_t end)</code> | | | <code>bool SamFile::SetReadSection(int32_t refID, int32_t start, int32_t end)</code> |
− | | Sets what part of the BAM file should be read. Fails if this is not a BAM file &/or the index file has not yet been read. This version will set it to only read a specific reference id and start(inclusive)/end(exclusive) region. The records for this section will be retrieved on each <code>ReadRecord</code> call. When all records have been retrieved for the specified section, ReadRecord will return failure until a new read section is set. | + | | Sets what part of the BAM file should be read. Fails if this is not a BAM file &/or the index file has not yet been read. This version will set it to only read a specific reference id and 0-based start(inclusive)/end(exclusive) region. The records for this section will be retrieved on each <code>ReadRecord</code> call. When all records have been retrieved for the specified section, ReadRecord will return failure until a new read section is set. |
| Pass in -1 in order to read the section of the bam file not associated with any reference ID. | | Pass in -1 in order to read the section of the bam file not associated with any reference ID. |
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| | <code>bool SamFile::SetReadSection(const char* refName, int32_t start, int32_t end)</code> | | | <code>bool SamFile::SetReadSection(const char* refName, int32_t start, int32_t end)</code> |
− | | Sets what part of the BAM file should be read. Fails if this is not a BAM file &/or the index file has not yet been read. This version will set it to only read a specific reference name and start(inclusive)/end(exclusive) region. The records for this section will be retrieved on each <code>ReadRecord</code> call. When all records have been retrieved for the specified section, ReadRecord will return failure until a new read section is set. | + | | Sets what part of the BAM file should be read. Fails if this is not a BAM file &/or the index file has not yet been read. This version will set it to only read a specific reference name and 0-based start(inclusive)/end(exclusive) region. The records for this section will be retrieved on each <code>ReadRecord</code> call. When all records have been retrieved for the specified section, ReadRecord will return failure until a new read section is set. |
| Pass in "" or "*" in order to read the section of the bam file not associated with any reference name. | | Pass in "" or "*" in order to read the section of the bam file not associated with any reference name. |
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| Return Value: true = success; false = failure. | | Return Value: true = success; false = failure. |
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| + | | <code>uint32_t SamFile::GetNumOverlaps(SamRecord& samRecord)</code> |
| + | | Returns the number of bases in the passed in read that overlap the region that is currently set for this file. |
| + | | Overlapping means that the bases occur in both the read and the reference as either matches or mismatches. This does not count insertions, deletions, clips, pads, or skips. |
| |} | | |} |
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