Difference between revisions of "SAM/BAM Classes FAQs"
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== How Do I? == | == How Do I? == | ||
| − | ===== Q: Map between a query/read sequence and a reference sequence to do things like looking up a base/quality at a given reference position or looking up a reference base for a given read position?===== | + | ===== Q: Map between a query/read sequence and a reference sequence to do things like looking up a base/quality at a given reference position or looking up a reference base for a given read position? ===== |
* A: Use [[C++ Class: CigarRoller#Mapping Between Reference and Read/Query|CigarRoller::getQueryIndex & CigarRoller::getRefOffset]] | * A: Use [[C++ Class: CigarRoller#Mapping Between Reference and Read/Query|CigarRoller::getQueryIndex & CigarRoller::getRefOffset]] | ||
| + | |||
| + | ===== Q: Read only portions of a sorted & indexed BAM file that fall within a specified region? ===== | ||
| + | * A: | ||
| + | *# open a sorted and indexed BAM file for reading (<code>SamFile::OpenForRead</code>) | ||
| + | *# read the BAM Index file (<code>SamFile::ReadBamIndex</code>) | ||
| + | *# read the header (<code>SamFile::ReadHeader</code>) | ||
| + | *# set the region to be read (<code>SamFile::SetReadSection</code>) | ||
| + | *# Loop calling <code>SamFile::ReadRecord</code> until it returns false - indicating there are no more reads within this region. | ||
| + | These methods are found in [[C++ Class: SamFile]]. | ||
| + | |||
| + | NOTE: ReadRecord will also return false on an error - use <code>SamFile::GetStatus()</code> to determine if it was an error or the end of the region. <code>GetStatus</code> returns SamStatus::NO_MORE_RECS for the end of the region. | ||
| + | |||
| + | * Q: How do I read multiple regions? | ||
| + | ** A: Use the above solution, but loop on the SetReadSection/ReadRecord steps until all sections have been processed. | ||
| + | |||
| + | ===== Q: Get additional information on this library? ===== | ||
| + | * A: Email me, Mary Kate, at mktrost@umich.edu. | ||
Revision as of 17:49, 29 July 2010
How Do I?
Q: Map between a query/read sequence and a reference sequence to do things like looking up a base/quality at a given reference position or looking up a reference base for a given read position?
Q: Read only portions of a sorted & indexed BAM file that fall within a specified region?
- A:
- open a sorted and indexed BAM file for reading (
SamFile::OpenForRead) - read the BAM Index file (
SamFile::ReadBamIndex) - read the header (
SamFile::ReadHeader) - set the region to be read (
SamFile::SetReadSection) - Loop calling
SamFile::ReadRecorduntil it returns false - indicating there are no more reads within this region.
- open a sorted and indexed BAM file for reading (
These methods are found in C++ Class: SamFile.
NOTE: ReadRecord will also return false on an error - use SamFile::GetStatus() to determine if it was an error or the end of the region. GetStatus returns SamStatus::NO_MORE_RECS for the end of the region.
- Q: How do I read multiple regions?
- A: Use the above solution, but loop on the SetReadSection/ReadRecord steps until all sections have been processed.
Q: Get additional information on this library?
- A: Email me, Mary Kate, at mktrost@umich.edu.
