libStatGen Software
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Class for extracting information from a SAM Flag. More...
#include <SamRecordHelper.h>
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static int | checkSequence (SamRecord &record, int32_t pos0Based, const char *sequence) |
Helper method that checks if the record's read sequence starting at the specified 0-based reference position matches the passed in sequence. More... | |
static bool | genSamTagsString (SamRecord &record, String &returnString, char delim='\t') |
Helper to append the SAM string representation of all the tags to the specified string. More... | |
static bool | genSamTagString (const char *tag, char vtype, void *value, String &returnString) |
Helper to append the SAM string representation of the specified tag to the specified string. More... | |
Class for extracting information from a SAM Flag.
Definition at line 24 of file SamRecordHelper.h.
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Helper method that checks if the record's read sequence starting at the specified 0-based reference position matches the passed in sequence.
Definition at line 21 of file SamRecordHelper.cpp.
References SamRecord::get0BasedPosition(), SamRecord::getCigarInfo(), Cigar::getQueryIndex(), SamRecord::getSequence(), and Cigar::INDEX_NA.
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Helper to append the SAM string representation of all the tags to the specified string.
Does NOT add a preceding delimiter before the first tag.
record | record whose tags to append. |
returnString | string to append the tags to. |
delim | delimiter to use to separate different tags. |
Definition at line 56 of file SamRecordHelper.cpp.
References genSamTagString(), SamRecord::getNextSamTag(), and SamRecord::resetTagIter().
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Helper to append the SAM string representation of the specified tag to the specified string.
tag | the tag name. |
vtype | the vtype. |
value | pointer to the value of the tag (will be cast to int, double, char, or string based on vtype). |
returnString | string to append the tag to. |
Definition at line 86 of file SamRecordHelper.cpp.
References SamRecord::isCharType(), SamRecord::isFloatType(), SamRecord::isIntegerType(), and SamRecord::isStringType().
Referenced by genSamTagsString().