libStatGen Software
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Class for parsing/creating/operating on SAM/BAM record tags. More...
#include <SamTags.h>
Constants for parsing tags. | |
static const char * | BQ_TAG = "BQ" |
static const char | BQ_TAG_TYPE = 'Z' |
static const char * | MD_TAG = "MD" |
static const char | MD_TAG_TYPE = 'Z' |
static const char * | ORIG_POS_TAG = "OP" |
static const char | ORIG_POS_TAG_TYPE = 'i' |
static const char * | ORIG_CIGAR_TAG = "OC" |
static const char | ORIG_CIGAR_TAG_TYPE = 'Z' |
static const char * | ORIG_QUAL_TAG = "OQ" |
static const char | ORIG_QUAL_TAG_TYPE = 'Z' |
static bool | createMDTag (String &outputMDtag, SamRecord &inputRec, GenomeSequence &genome) |
Create the MD tag for the specified input record and the genome. More... | |
static bool | isMDTagCorrect (SamRecord &inputRec, GenomeSequence &genome) |
Check to see if the MD tag in the record is accurate. | |
static bool | updateMDTag (SamRecord &inputRec, GenomeSequence &genome) |
Class for parsing/creating/operating on SAM/BAM record tags.
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Create the MD tag for the specified input record and the genome.
Definition at line 34 of file SamTags.cpp.
References BaseUtilities::areEqual(), SamRecord::get0BasedPosition(), SamRecord::getCigarInfo(), Cigar::getExpectedReferenceBaseCount(), GenomeSequence::getGenomePosition(), Cigar::getQueryIndex(), SamRecord::getReferenceName(), SamRecord::getSequence(), Cigar::INDEX_NA, and BaseUtilities::isAmbiguous().
Referenced by isMDTagCorrect(), and SamValidator::isValidTags().