C++ Class: SamFile - Revision history

Ppwhite: /* SamFileWriter */

2017-02-02T15:03:54Z

SamFileWriter

← Older revision		Revision as of 11:03, 2 February 2017
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	=== SamFileWriter ===		=== SamFileWriter ===
	http://~~www~~.sph.umich.edu/~~csg~~/mktrost/doxygen/current/classSamFileWriter.html		http://csg.sph.umich.edu//mktrost/doxygen/current/classSamFileWriter.html

	== Statistics ==		== Statistics ==

2017-02-02T15:03:38Z

SamFileReader

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	== Child Classes ==		== Child Classes ==
	=== SamFileReader ===		=== SamFileReader ===
	http://~~www~~.sph.umich.edu/~~csg~~/mktrost/doxygen/current/classSamFileReader.html		http://csg.sph.umich.edu//mktrost/doxygen/current/classSamFileReader.html

	=== SamFileWriter ===		=== SamFileWriter ===

2017-02-02T15:03:23Z

Class Documentation

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	=== Class Documentation ===		=== Class Documentation ===

	See: http://~~www~~.sph.umich.edu/~~csg~~/mktrost/doxygen/current/classSamFile.html		See: http://csg.sph.umich.edu//mktrost/doxygen/current/classSamFile.html

	== Child Classes ==		== Child Classes ==

2011-08-24T17:31:34Z

2010-11-17T20:16:47Z

2010-11-02T05:49:34Z

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	[[Category:~~libbam~~]]		[[Category:Software]]
			[[Category:C++]]
			[[Category:libStatGen]]
			[[Category:libStatGen BAM]]

	== Reading/Writing SAM/BAM Files In Your Program ==		== Reading/Writing SAM/BAM Files In Your Program ==
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	'''Future Enhancements:''' Add the ability to read alignments that match a given start, end position for a specific reference sequence.		'''Future Enhancements:''' Add the ability to read alignments that match a given start, end position for a specific reference sequence.

	This class is part of [[C++ Library: ~~libbam~~\|~~libbam~~]].		This class is part of [[C++ Library: libStatGen\|C++ Library: libStatGen]].

	=== Class Methods ===		=== Class Methods ===

2010-08-26T14:38:16Z

Statistic Generation

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	\|TotalBases		\|TotalBases
	\| Sum of the SEQ lengths for all alignments that were successfully read from the file.		\| Sum of the SEQ lengths for all alignments that were successfully read from the file.
			NOTE: Includes bases that are 'N'.
	\|-		\|-
	\|BasesInMappedReads		\|BasesInMappedReads
	\| Sum of the SEQ lengths for all alignments that were successfully read from the file with FLAG bit 0x004 set to 0 (not unmapped).		\| Sum of the SEQ lengths for all alignments that were successfully read from the file with FLAG bit 0x004 set to 0 (not unmapped).
			NOTE: Includes bases that are 'N'.
	\|}		\|}

2010-08-23T21:22:24Z

← Older revision		Revision as of 17:22, 23 August 2010
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	\| <code>uint32_t SamFile::GetNumOverlaps(SamRecord& samRecord)</code>		\| <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.		\| 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.		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.
			\|-
			\| <code>void SamFile::GenerateStatistics(bool genStats)</code>
			\| Set this SamFile class to record statistic information as records are read from the file.
			\|-
			\| <code>inline void SamFile::PrintStatistics()</code>
			\| Print the statistics that have been recorded (by calling GenerateStatistics)
	\|}		\|}

2010-08-23T21:20:32Z

← Older revision		Revision as of 17:20, 23 August 2010
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	\| <code>uint32_t SamFile::GetNumOverlaps(SamRecord& samRecord)</code>		\| <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.		\| 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.		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.
	\|}		\|}

2010-08-23T21:19:40Z

Statistic Generation

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 NOTE: If the TotalReads is greater than 10^6, then the Read Counts and Base Counts specify the total counts divided by 10^6.  This is indicated in the output with a (e6) appended to the field name.
 == Usage Examples ==
 [[Sam Library Usage Examples]]