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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.
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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