BwaMemAligner (gatk-bwamem-jni 1.0.5 API)

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

All Implemented Interfaces:

java.lang.AutoCloseable
```
public final class BwaMemAligner
extends java.lang.Object
implements java.lang.AutoCloseable
```
Given an open index, this class lets you do alignment of sequences. Don't forget to close it, or you'll leak a little memory. Usage pattern: Create a BwaMemAligner on some BwaMemIndex Set your bwa-mem parameters Align 1 or more chunks of sequences with alignSeqs Close the BwaMemAligner This class is not thread-safe, but it's very light-weight: just use a separate instance in each thread.

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`MEM_F_ALL`
`static int`	`MEM_F_NO_MULTI`
`static int`	`MEM_F_NO_RESCUE`
`static int`	`MEM_F_NOPAIRING`
`static int`	`MEM_F_PE`
`static int`	`MEM_F_PRIMARY5`
`static int`	`MEM_F_REF_HDR`
`static int`	`MEM_F_SMARTPE`
`static int`	`MEM_F_SOFTCLIP`

Constructor Summary

Constructors
Constructor and Description

BwaMemAligner(BwaMemIndex index)

Constructors
Constructor and Description
`BwaMemAligner(BwaMemIndex index)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`alignPairs()`
`<T> java.util.List<java.util.List<BwaMemAlignment>>`	`alignSeqs(java.lang.Iterable<T> iterable, java.util.function.Function<T,byte[]> func)` A more abstract version that takes an iterable of things that can be turned into a byte[] of base calls.
`java.util.List<java.util.List<BwaMemAlignment>>`	`alignSeqs(java.util.List<byte[]> sequences)` Just align some sequences.
`void`	`close()`
`void`	`dontInferPairEndStats()` Tells the aligner to avoid trying to infer inter-size stats and just go with bwamem defaults when that information is not-available.
`int`	`getBandwidthOption()`
`int`	`getChunkSizeOption()`
`int`	`getClip3PenaltyOption()`
`int`	`getClip5PenaltyOption()`
`int`	`getDGapExtendPenaltyOption()`
`int`	`getDGapOpenPenaltyOption()`
`float`	`getDropRatioOption()`
`int`	`getFlagOption()`
`int`	`getIGapExtendPenaltyOption()`
`int`	`getIGapOpenPenaltyOption()`
`BwaMemIndex`	`getIndex()`
`int`	`getMapQCoefFacOption()`
`float`	`getMapQCoefLenOption()`
`float`	`getMaskLevelOption()`
`float`	`getMaskLevelRedunOption()`
`int`	`getMatchScoreOption()`
`int`	`getMaxChainExtendOption()`
`int`	`getMaxChainGapOption()`
`int`	`getMaxInsOption()`
`int`	`getMaxMateSWOption()`
`long`	`getMaxMemIntvOption()`
`int`	`getMaxSeedOccurencesOption()`
`int`	`getMaxXAHitsAltOption()`
`int`	`getMaxXAHitsOption()`
`int`	`getMinChainWeightOption()`
`int`	`getMinSeedLengthOption()`
`int`	`getMismatchPenaltyOption()`
`int`	`getNThreadsOption()`
`int`	`getOutputScoreThresholdOption()`
`byte[]`	`getScoringMatrixOption()`
`float`	`getSplitFactorOption()`
`int`	`getSplitWidthOption()`
`int`	`getUnpairedPenaltyOption()`
`float`	`getXADropRatio()`
`int`	`getZDropOption()`
`void`	`inferPairEndStats()` Indicate that we want bwa-mem to infer pair-end inter-size stat from the sequences given.
`boolean`	`isOpen()`
`void`	`setBandwidthOption(int w)`
`void`	`setChunkSizeOption(int chunk_size)`
`void`	`setClip3PenaltyOption(int pen_clip3)`
`void`	`setClip5PenaltyOption(int pen_clip5)`
`void`	`setDGapExtendPenaltyOption(int e_del)`
`void`	`setDGapOpenPenaltyOption(int o_del)`
`void`	`setDropRatioOption(float drop_ratio)`
`void`	`setFlagOption(int flag)`
`void`	`setIGapExtendPenaltyOption(int e_ins)`
`void`	`setIGapOpenPenaltyOption(int o_ins)`
`void`	`setIntraCtgOptions()`
`void`	`setMapQCoefFacOption(int mapQ_coef_fac)`
`void`	`setMapQCoefLenOption(float mapQ_coef_len)`
`void`	`setMaskLevelRedunOption(float max_level_redun)`
`void`	`setMatchScoreOption(int a)`
`void`	`setMaxChainExtendOption(int max_chain_extend)`
`void`	`setMaxChainGapOption(int max_chain_gap)`
`void`	`setMaxInsOption(int max_ins)`
`void`	`setMaxLevelOption(float max_level)`
`void`	`setMaxMateSWOption(int max_matesw)`
`void`	`setMaxMemIntvOption(long max_mem_intv)`
`void`	`setMaxSeedOccurencesOption(int max_occ)`
`void`	`setMaxXAHitsAltOption(int max_XA_hits_alt)`
`void`	`setMaxXAHitsOption(int max_XA_hits)`
`void`	`setMinChainWeightOption(int min_chain_weight)`
`void`	`setMinSeedLengthOption(int min_seed_len)`
`void`	`setMismatchPenaltyOption(int b)`
`void`	`setNThreadsOption(int n_threads)`
`void`	`setOutputScoreThresholdOption(int T)`
`void`	`setProperPairEndStats(BwaMemPairEndStats stats)` Indicate the pair-end inter size stats for "properly" oriented read-pairs.
`void`	`setScoringMatrixOption(byte[] mat)`
`void`	`setSplitFactorOption(float split_factor)`
`void`	`setSplitWidthOption(int split_width)`
`void`	`setUnpairedPenaltyOption(int pen_unpaired)`
`void`	`setXADropRatio(float XA_drop_ratio)`
`void`	`setZDropOption(int zdrop)`

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

Field Detail
- MEM_F_PE
```
public static final int MEM_F_PE
```
  See Also:
  
  Constant Field Values
- MEM_F_NOPAIRING
```
public static final int MEM_F_NOPAIRING
```
  See Also:
  
  Constant Field Values
- MEM_F_ALL
```
public static final int MEM_F_ALL
```
  See Also:
  
  Constant Field Values
- MEM_F_NO_MULTI
```
public static final int MEM_F_NO_MULTI
```
  See Also:
  
  Constant Field Values
- MEM_F_NO_RESCUE
```
public static final int MEM_F_NO_RESCUE
```
  See Also:
  
  Constant Field Values
- MEM_F_REF_HDR
```
public static final int MEM_F_REF_HDR
```
  See Also:
  
  Constant Field Values
- MEM_F_SOFTCLIP
```
public static final int MEM_F_SOFTCLIP
```
  See Also:
  
  Constant Field Values
- MEM_F_SMARTPE
```
public static final int MEM_F_SMARTPE
```
  See Also:
  
  Constant Field Values
- MEM_F_PRIMARY5
```
public static final int MEM_F_PRIMARY5
```
  See Also:
  
  Constant Field Values

Constructor Detail

BwaMemAligner

public BwaMemAligner(BwaMemIndex index)

Method Detail

isOpen
```
public boolean isOpen()
```

close
```
public void close()
```
Specified by:

close in interface java.lang.AutoCloseable

getMatchScoreOption
```
public int getMatchScoreOption()
```

setMatchScoreOption

public void setMatchScoreOption(int a)

getMismatchPenaltyOption
```
public int getMismatchPenaltyOption()
```

setMismatchPenaltyOption

public void setMismatchPenaltyOption(int b)

getDGapOpenPenaltyOption
```
public int getDGapOpenPenaltyOption()
```

setDGapOpenPenaltyOption

public void setDGapOpenPenaltyOption(int o_del)

getDGapExtendPenaltyOption

public int getDGapExtendPenaltyOption()

setDGapExtendPenaltyOption

public void setDGapExtendPenaltyOption(int e_del)

getIGapOpenPenaltyOption
```
public int getIGapOpenPenaltyOption()
```

setIGapOpenPenaltyOption

public void setIGapOpenPenaltyOption(int o_ins)

getIGapExtendPenaltyOption

public int getIGapExtendPenaltyOption()

setIGapExtendPenaltyOption

public void setIGapExtendPenaltyOption(int e_ins)

getUnpairedPenaltyOption
```
public int getUnpairedPenaltyOption()
```

setUnpairedPenaltyOption

public void setUnpairedPenaltyOption(int pen_unpaired)

getClip5PenaltyOption
```
public int getClip5PenaltyOption()
```

setClip5PenaltyOption

public void setClip5PenaltyOption(int pen_clip5)

getClip3PenaltyOption
```
public int getClip3PenaltyOption()
```

setClip3PenaltyOption

public void setClip3PenaltyOption(int pen_clip3)

getBandwidthOption
```
public int getBandwidthOption()
```

setBandwidthOption

public void setBandwidthOption(int w)

getZDropOption
```
public int getZDropOption()
```

setZDropOption

public void setZDropOption(int zdrop)

getMaxMemIntvOption
```
public long getMaxMemIntvOption()
```

setMaxMemIntvOption

public void setMaxMemIntvOption(long max_mem_intv)

getOutputScoreThresholdOption

public int getOutputScoreThresholdOption()

setOutputScoreThresholdOption

public void setOutputScoreThresholdOption(int T)

alignPairs
```
public void alignPairs()
```

getFlagOption
```
public int getFlagOption()
```

setFlagOption
```
public void setFlagOption(int flag)
```

getMinSeedLengthOption
```
public int getMinSeedLengthOption()
```

setMinSeedLengthOption

public void setMinSeedLengthOption(int min_seed_len)

getMinChainWeightOption
```
public int getMinChainWeightOption()
```

setMinChainWeightOption

public void setMinChainWeightOption(int min_chain_weight)

getMaxChainExtendOption
```
public int getMaxChainExtendOption()
```

setMaxChainExtendOption

public void setMaxChainExtendOption(int max_chain_extend)

getSplitFactorOption
```
public float getSplitFactorOption()
```

setSplitFactorOption

public void setSplitFactorOption(float split_factor)

getSplitWidthOption
```
public int getSplitWidthOption()
```

setSplitWidthOption

public void setSplitWidthOption(int split_width)

getMaxSeedOccurencesOption

public int getMaxSeedOccurencesOption()

setMaxSeedOccurencesOption

public void setMaxSeedOccurencesOption(int max_occ)

getMaxChainGapOption
```
public int getMaxChainGapOption()
```

setMaxChainGapOption

public void setMaxChainGapOption(int max_chain_gap)

getNThreadsOption
```
public int getNThreadsOption()
```

setNThreadsOption

public void setNThreadsOption(int n_threads)

getChunkSizeOption
```
public int getChunkSizeOption()
```

setChunkSizeOption

public void setChunkSizeOption(int chunk_size)

getMaskLevelOption
```
public float getMaskLevelOption()
```

setMaxLevelOption

public void setMaxLevelOption(float max_level)

getDropRatioOption
```
public float getDropRatioOption()
```

setDropRatioOption

public void setDropRatioOption(float drop_ratio)

getXADropRatio
```
public float getXADropRatio()
```

setXADropRatio

public void setXADropRatio(float XA_drop_ratio)

getMaskLevelRedunOption

public float getMaskLevelRedunOption()

setMaskLevelRedunOption

public void setMaskLevelRedunOption(float max_level_redun)

getMapQCoefLenOption
```
public float getMapQCoefLenOption()
```

setMapQCoefLenOption

public void setMapQCoefLenOption(float mapQ_coef_len)

getMapQCoefFacOption
```
public int getMapQCoefFacOption()
```

setMapQCoefFacOption

public void setMapQCoefFacOption(int mapQ_coef_fac)

getMaxInsOption
```
public int getMaxInsOption()
```

setMaxInsOption

public void setMaxInsOption(int max_ins)

getMaxMateSWOption
```
public int getMaxMateSWOption()
```

setMaxMateSWOption

public void setMaxMateSWOption(int max_matesw)

getMaxXAHitsOption
```
public int getMaxXAHitsOption()
```

setMaxXAHitsOption

public void setMaxXAHitsOption(int max_XA_hits)

getMaxXAHitsAltOption
```
public int getMaxXAHitsAltOption()
```

setMaxXAHitsAltOption

public void setMaxXAHitsAltOption(int max_XA_hits_alt)

getScoringMatrixOption

public byte[] getScoringMatrixOption()

setScoringMatrixOption

public void setScoringMatrixOption(byte[] mat)

setIntraCtgOptions
```
public void setIntraCtgOptions()
```

inferPairEndStats
```
public void inferPairEndStats()
```
Indicate that we want bwa-mem to infer pair-end inter-size stat from the sequences given. Only has effect in paired alignment.

dontInferPairEndStats
```
public void dontInferPairEndStats()
```
Tells the aligner to avoid trying to infer inter-size stats and just go with bwamem defaults when that information is not-available.

setProperPairEndStats
```
public void setProperPairEndStats(BwaMemPairEndStats stats)
```
Indicate the pair-end inter size stats for "properly" oriented read-pairs.

Parameters:

stats -

getIndex
```
public BwaMemIndex getIndex()
```

alignSeqs
```
public java.util.List<java.util.List<BwaMemAlignment>> alignSeqs(java.util.List<byte[]> sequences)
```
Just align some sequences.

Parameters:

sequences - A list of byte[]'s that contain base calls (ASCII 'A', 'C', 'G', or 'T').

Returns:

A list of the same length as the input list. Each element is a list of alignments for the corresponding sequence.

alignSeqs
```
public <T> java.util.List<java.util.List<BwaMemAlignment>> alignSeqs(java.lang.Iterable<T> iterable,
                                                                     java.util.function.Function<T,byte[]> func)
```
A more abstract version that takes an iterable of things that can be turned into a byte[] of base calls.

Type Parameters:

T - The read-like thing.

Parameters:

iterable - An iterable over something like a read, that contains a sequence.

func - A lambda that picks the sequence out of your read-like thing.

Returns:

A list of (possibly multiple) alignments for each input sequence.

Class BwaMemAligner

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

MEM_F_PE

MEM_F_NOPAIRING

MEM_F_ALL

MEM_F_NO_MULTI

MEM_F_NO_RESCUE

MEM_F_REF_HDR

MEM_F_SOFTCLIP

MEM_F_SMARTPE

MEM_F_PRIMARY5

Constructor Detail

BwaMemAligner

Method Detail

isOpen

close

getMatchScoreOption

setMatchScoreOption

getMismatchPenaltyOption

setMismatchPenaltyOption

getDGapOpenPenaltyOption

setDGapOpenPenaltyOption

getDGapExtendPenaltyOption

setDGapExtendPenaltyOption

getIGapOpenPenaltyOption

setIGapOpenPenaltyOption

getIGapExtendPenaltyOption

setIGapExtendPenaltyOption

getUnpairedPenaltyOption

setUnpairedPenaltyOption

getClip5PenaltyOption

setClip5PenaltyOption

getClip3PenaltyOption

setClip3PenaltyOption

getBandwidthOption

setBandwidthOption

getZDropOption

setZDropOption

getMaxMemIntvOption

setMaxMemIntvOption

getOutputScoreThresholdOption

setOutputScoreThresholdOption

alignPairs

getFlagOption

setFlagOption

getMinSeedLengthOption

setMinSeedLengthOption

getMinChainWeightOption

setMinChainWeightOption

getMaxChainExtendOption

setMaxChainExtendOption

getSplitFactorOption

setSplitFactorOption

getSplitWidthOption

setSplitWidthOption

getMaxSeedOccurencesOption

setMaxSeedOccurencesOption

getMaxChainGapOption

setMaxChainGapOption

getNThreadsOption

setNThreadsOption

getChunkSizeOption

setChunkSizeOption

getMaskLevelOption

setMaxLevelOption

getDropRatioOption

setDropRatioOption

getXADropRatio

setXADropRatio

getMaskLevelRedunOption

setMaskLevelRedunOption

getMapQCoefLenOption

setMapQCoefLenOption

getMapQCoefFacOption

setMapQCoefFacOption

getMaxInsOption