libStatGen Software
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Class for extracting information from a SAM Flag. More...
#include <SamFlag.h>
Static methods for determining the contents of a flag. | |
static bool | isMapped (uint16_t flag) |
static bool | isMateMapped (uint16_t flag) |
static bool | isPaired (uint16_t flag) |
static bool | isReverse (uint16_t flag) |
static bool | isMateReverse (uint16_t flag) |
static bool | isProperPair (uint16_t flag) |
static bool | isDuplicate (uint16_t flag) |
static bool | isQCFailure (uint16_t flag) |
static bool | isSecondary (uint16_t flag) |
static bool | isFirstFragment (uint16_t flag) |
Return if it is the first fragment or not (if FIRST_READ is set and SECOND_READ is not). | |
static bool | isLastFragment (uint16_t flag) |
Return if it is the last fragment or not (if FIRST_READ is not set and SECOND_READ is). | |
static bool | isMidFragment (uint16_t flag) |
Return if it is a middle fragment or not (if FIRST_READ is set and SECOND_READ is also set). | |
static bool | isUnknownFragment (uint16_t flag) |
Return if it is an unknown fragment fragment or not (if FIRST_READ is not set and SECOND_READ is also not set). | |
static uint8_t | getFragmentType (uint16_t flag) |
static void | setUnmapped (uint16_t &flag) |
Mark the passed in flag as unmapped. | |
static void | setNotDuplicate (uint16_t &flag) |
Mark the passed in flag as not duplicate. | |
static void | setDuplicate (uint16_t &flag) |
Mark the passed in flag as not duplicate. | |