1,120
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchSAM/BAM Classes FAQs (view source)
Revision as of 17:20, 11 September 2021
, 17:20, 11 September 2021no edit summary
[[Category:libStatGen]]
[[Category:libStatGen BAM]]
== How Do I? ==
== How Do I? ==
===== Q: What is SAM/BAM? =====
* A: See: [[SAM]] and [[BAM]]. [[SAM]] also provides additional details as to what is a CIGAR, QUALITY, and TAG.
===== 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|Cigar::getQueryIndex & Cigar::getRefOffset]]
===== Q: Read only portions of a sorted & indexed BAM file that fall within a specified region? =====
===== Q: Read only portions of a sorted & indexed BAM file that fall within a specified region? =====
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.
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.
See the library usage page for an [[Sam_Library_Usage_Examples#Read_a_Specified_Region_from_a_Sorted_.26_Indexed_BAM_File|Example]].
* Q: How do I read multiple regions?
* Q: How do I read multiple regions?
===== Q: Get additional information on this library? =====
===== Q: Get additional information on this library? =====
* A: Email me, Mary Kate, at mktrost@umich.edu.
* A: If you have any questions or comments, please raise issue in [https://github.com/statgen/ our GitHub repositories].
