SAM/BAM Classes FAQs - Revision history

Hmkang at 21:20, 11 September 2021

2021-09-11T21:20:17Z

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	===== Q: Get additional information on this library? =====		===== Q: Get additional information on this library? =====
	* A: If you have any questions or comments, please raise issue in ~~the corresponding~~ [https://github.com/statgen/ our GitHub repositories].		* A: If you have any questions or comments, please raise issue in [https://github.com/statgen/ our GitHub repositories].

2021-09-11T21:19:55Z

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	===== 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 the corresponding [https://github.com/statgen/ our GitHub repositories].

2010-11-02T05:48:06Z

2010-11-02T05:45:57Z

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(No difference)

2010-08-11T12:39:15Z

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	===== 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? =====

2010-08-02T15:33:04Z

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	===== Q: What is SAM/BAM? =====		===== Q: What is SAM/BAM? =====
	* A: See: [[SAM]] and [[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? =====

2010-08-02T15:32:12Z

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	== How Do I? ==		== How Do I? ==

			===== Q: What is SAM/BAM? =====
			* A: See: [[SAM]] and [[BAM]]

	===== 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? =====

2010-08-02T14:44:10Z

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	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?

2010-07-29T21:49:49Z

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 == 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]]

2010-07-29T21:26:48Z

← Older revision		Revision as of 17:26, 29 July 2010
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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]]