public final class BwaMemPairEndStats
extends java.lang.Object
// bwamem.h
typedef struct {
int low, high; // lower and upper bounds within which a read pair is considered to be properly paired
int failed; // non-zero if the orientation is not supported by sufficient data
double avg, std; // mean and stddev of the insert size distribution
} mem_pestat_t;
| Modifier and Type | Field and Description |
|---|---|
double |
average
The average insert size.
|
static int |
DEFAULT_LOW_AND_HIGH_SIGMA
Default number of std.
|
static double |
DEFAULT_STD_TO_AVERAGE_RATIO
Default std.
|
static BwaMemPairEndStats |
DO_NOT_INFER
Constant to indicate that pair-end insert size inference failed or hat is should not be inferred depending on
the context.
|
boolean |
failed
Depending on the context, indicates iff the insert-size inference failed or
if we are requesting not to perform such a inference.
|
static BwaMemPairEndStats |
FAILED
Constant to indicate that pair-end insert size inference failed or that it should not be inferred depending on
the context.
|
int |
high
The longest insert size that is considered normal.
|
int |
low
The shortest insert size that is considered normal.
|
double |
std
The insert size std.
|
| Constructor and Description |
|---|
BwaMemPairEndStats(double average)
Composes a new instance given the estimated average.
|
BwaMemPairEndStats(double average,
double std)
Composes a new instance given the estimated average and std.
|
BwaMemPairEndStats(double average,
double std,
int low,
int high)
|
| Modifier and Type | Method and Description |
|---|---|
boolean |
equals(BwaMemPairEndStats other) |
boolean |
equals(java.lang.Object other) |
int |
hashCode() |
java.lang.String |
toString() |
public static final int DEFAULT_LOW_AND_HIGH_SIGMA
Its value, 4, corresponds to the one use in bwa-mem source code at the time this code was written.
public static final double DEFAULT_STD_TO_AVERAGE_RATIO
Its value, 0.1, corresponds to the one use in bwa-mem source code at the time this code was written.
public static final BwaMemPairEndStats FAILED
public static final BwaMemPairEndStats DO_NOT_INFER
public final int low
public final int high
failed is false, and if so is always in the [#average .. +Inf) range.public final boolean failed
true, nothing can be expected on what values other fields take.public final double average
failed is false, and if so is always in the range [1 .. +Inf).public final double std
failed is false, and if so is finite and equal or greater than 0.public BwaMemPairEndStats(double average,
double std)
low and high limits are calculated using the recipe use in bwa mem's code-base where the 4th sigma is used as the upper limit rounding it to the closest integer.
The resulting stats object's failed field will be set to false.
average - the insert size average estimate.std - the insert size standard deviation estimate.java.lang.IllegalArgumentException - if either input is Double.NaN, infinite. Also if the average is
less than 1.0 and if the std. deviation is strictly negative.public BwaMemPairEndStats(double average)
The std. deviation would be calculated out of this mean using the default deviation
to average ratio DEFAULT_STD_TO_AVERAGE_RATIO.
The resulting stats object's failed field will be set to false.
Low and high insert-sizes will be estimated using the approach described in BwaMemPairEndStats(double, double).
The resulting stats object's failed field will be set to false.
average - the insert size average estimate.java.lang.IllegalArgumentException - if the input average is Double.NaN, infinite or less than 1.public BwaMemPairEndStats(double average,
double std,
int low,
int high)
average, std, low and high.
The resulting stats object's failed field will be set to false.
average - the insert-size average in [1 .. +Inf) range.std - the insert-size std. dev in [0 .. +Inf) range.low - the shortest insert-size to be considered "normal" [1 .. average]high - the longest insert-size to be considered "normal" [average .. +Inf).java.lang.IllegalArgumentException - if the values provided are invalid or inconsistent based on the constraints
listed above.public java.lang.String toString()
toString in class java.lang.Objectpublic boolean equals(java.lang.Object other)
equals in class java.lang.Objectpublic int hashCode()
hashCode in class java.lang.Objectpublic boolean equals(BwaMemPairEndStats other)