BwaMemPairEndStats (gatk-bwamem-jni 1.0.5 API)

java.lang.Object
- org.broadinstitute.hellbender.utils.bwa.BwaMemPairEndStats

public final class BwaMemPairEndStats
extends java.lang.Object

Equivalent to Bwa's mem_pestat_t struct. At the time this was written such a type declaration looked like this:

    // 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;

Field Summary

Fields
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 Summary

Constructors
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)` Composes a new instance giving arbitrary (albeit valid and consistent) values to all its numerical fields: `average`, `std`, `low` and `high`.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`equals(BwaMemPairEndStats other)`
`boolean`	`equals(java.lang.Object other)`
`int`	`hashCode()`
`java.lang.String`	`toString()`

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

- Field Detail
  - DEFAULT_LOW_AND_HIGH_SIGMA
```
public static final int DEFAULT_LOW_AND_HIGH_SIGMA
```
    Default number of std. deviation from the mean for the lowest and highest insert size that is considered normal.
    Its value, 4, corresponds to the one use in bwa-mem source code at the time this code was written.
    
    See Also:
    
    Constant Field Values
  - DEFAULT_STD_TO_AVERAGE_RATIO
```
public static final double DEFAULT_STD_TO_AVERAGE_RATIO
```
    Default std. deviation to average ratio to use in case the deviation is not provided.
    Its value, 0.1, corresponds to the one use in bwa-mem source code at the time this code was written.
    
    See Also:
    
    Constant Field Values
  - FAILED
```
public static final BwaMemPairEndStats FAILED
```
    Constant to indicate that pair-end insert size inference failed or that it should not be inferred depending on the context.
  - DO_NOT_INFER
```
public static final 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.
  - low
```
public final int low
```
    The shortest insert size that is considered normal.
    Only defined if failed is false, and if so is always in the [1..average] range.
  - high
```
public final int high
```
    The longest insert size that is considered normal.
    Only defined if failed is false, and if so is always in the [#average .. +Inf) range.
  - failed
```
public final boolean failed
```
    Depending on the context, indicates iff the insert-size inference failed or if we are requesting not to perform such a inference.
    When this field is true, nothing can be expected on what values other fields take.
  - average
```
public final double average
```
    The average insert size.
    Only defined if failed is false, and if so is always in the range [1 .. +Inf).
  - std
```
public final double std
```
    The insert size std. deviation.
    Only defined if failed is false, and if so is finite and equal or greater than 0.
- Constructor Detail
  - BwaMemPairEndStats
```
public BwaMemPairEndStats(double average,
                          double std)
```
    Composes a new instance given the estimated average and std. deviation
    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.
    
    Parameters:
    
    average - the insert size average estimate.
    
    std - the insert size standard deviation estimate.
    
    Throws:
    
    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.
  - BwaMemPairEndStats
```
public BwaMemPairEndStats(double average)
```
    Composes a new instance given the estimated 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.
    
    Parameters:
    
    average - the insert size average estimate.
    
    Throws:
    
    java.lang.IllegalArgumentException - if the input average is Double.NaN, infinite or less than 1.
  - BwaMemPairEndStats
```
public BwaMemPairEndStats(double average,
                          double std,
                          int low,
                          int high)
```
    Composes a new instance giving arbitrary (albeit valid and consistent) values to all its numerical fields: average, std, low and high.
    The resulting stats object's failed field will be set to false.
    
    Parameters:
    
    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).
    
    Throws:
    
    java.lang.IllegalArgumentException - if the values provided are invalid or inconsistent based on the constraints listed above.
- Method Detail
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object
  - equals
```
public boolean equals(java.lang.Object other)
```
    Overrides:
    
    equals in class java.lang.Object
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class java.lang.Object
  - equals
```
public boolean equals(BwaMemPairEndStats other)
```

Class BwaMemPairEndStats

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

DEFAULT_LOW_AND_HIGH_SIGMA

DEFAULT_STD_TO_AVERAGE_RATIO

FAILED

DO_NOT_INFER

low

high

failed

average

std

Constructor Detail

BwaMemPairEndStats

BwaMemPairEndStats

BwaMemPairEndStats

Method Detail

toString

equals

hashCode

equals