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Field Summary
Fields
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
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Method Summary
int
Alignments are categorized as primary or secondary (alternate).
Retrieve an identifying String that can be used for later access.
long
Retrieve the projected length of an Alignment projected upon Reference.
long
Retrieve the Alignment's starting position on the Reference
getClippedFragmentQualities
boolean
Test if orientation is reversed with respect to the Reference sequence.
int
boolean
getMateIsReversedOrientation
char
int
long
boolean
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Method Details
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getClippedFragmentQualities
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getMateIsReversedOrientation