public final class BwaMemAligner
extends java.lang.Object
implements java.lang.AutoCloseable
| 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 and Description |
|---|
BwaMemAligner(BwaMemIndex index) |
| 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) |
public static final int MEM_F_PE
public static final int MEM_F_NOPAIRING
public static final int MEM_F_ALL
public static final int MEM_F_NO_MULTI
public static final int MEM_F_NO_RESCUE
public static final int MEM_F_REF_HDR
public static final int MEM_F_SOFTCLIP
public static final int MEM_F_SMARTPE
public static final int MEM_F_PRIMARY5
public BwaMemAligner(BwaMemIndex index)
public boolean isOpen()
public void close()
close in interface java.lang.AutoCloseablepublic int getMatchScoreOption()
public void setMatchScoreOption(int a)
public int getMismatchPenaltyOption()
public void setMismatchPenaltyOption(int b)
public int getDGapOpenPenaltyOption()
public void setDGapOpenPenaltyOption(int o_del)
public int getDGapExtendPenaltyOption()
public void setDGapExtendPenaltyOption(int e_del)
public int getIGapOpenPenaltyOption()
public void setIGapOpenPenaltyOption(int o_ins)
public int getIGapExtendPenaltyOption()
public void setIGapExtendPenaltyOption(int e_ins)
public int getUnpairedPenaltyOption()
public void setUnpairedPenaltyOption(int pen_unpaired)
public int getClip5PenaltyOption()
public void setClip5PenaltyOption(int pen_clip5)
public int getClip3PenaltyOption()
public void setClip3PenaltyOption(int pen_clip3)
public int getBandwidthOption()
public void setBandwidthOption(int w)
public int getZDropOption()
public void setZDropOption(int zdrop)
public long getMaxMemIntvOption()
public void setMaxMemIntvOption(long max_mem_intv)
public int getOutputScoreThresholdOption()
public void setOutputScoreThresholdOption(int T)
public void alignPairs()
public int getFlagOption()
public void setFlagOption(int flag)
public int getMinSeedLengthOption()
public void setMinSeedLengthOption(int min_seed_len)
public int getMinChainWeightOption()
public void setMinChainWeightOption(int min_chain_weight)
public int getMaxChainExtendOption()
public void setMaxChainExtendOption(int max_chain_extend)
public float getSplitFactorOption()
public void setSplitFactorOption(float split_factor)
public int getSplitWidthOption()
public void setSplitWidthOption(int split_width)
public int getMaxSeedOccurencesOption()
public void setMaxSeedOccurencesOption(int max_occ)
public int getMaxChainGapOption()
public void setMaxChainGapOption(int max_chain_gap)
public int getNThreadsOption()
public void setNThreadsOption(int n_threads)
public int getChunkSizeOption()
public void setChunkSizeOption(int chunk_size)
public float getMaskLevelOption()
public void setMaxLevelOption(float max_level)
public float getDropRatioOption()
public void setDropRatioOption(float drop_ratio)
public float getXADropRatio()
public void setXADropRatio(float XA_drop_ratio)
public float getMaskLevelRedunOption()
public void setMaskLevelRedunOption(float max_level_redun)
public float getMapQCoefLenOption()
public void setMapQCoefLenOption(float mapQ_coef_len)
public int getMapQCoefFacOption()
public void setMapQCoefFacOption(int mapQ_coef_fac)
public int getMaxInsOption()
public void setMaxInsOption(int max_ins)
public int getMaxMateSWOption()
public void setMaxMateSWOption(int max_matesw)
public int getMaxXAHitsOption()
public void setMaxXAHitsOption(int max_XA_hits)
public int getMaxXAHitsAltOption()
public void setMaxXAHitsAltOption(int max_XA_hits_alt)
public byte[] getScoringMatrixOption()
public void setScoringMatrixOption(byte[] mat)
public void setIntraCtgOptions()
public void inferPairEndStats()
public void dontInferPairEndStats()
public void setProperPairEndStats(BwaMemPairEndStats stats)
stats - public BwaMemIndex getIndex()
public java.util.List<java.util.List<BwaMemAlignment>> alignSeqs(java.util.List<byte[]> sequences)
sequences - A list of byte[]'s that contain base calls (ASCII 'A', 'C', 'G', or 'T').public <T> java.util.List<java.util.List<BwaMemAlignment>> alignSeqs(java.lang.Iterable<T> iterable, java.util.function.Function<T,byte[]> func)
T - The read-like thing.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.