| Package | Description |
|---|---|
| picard.fingerprint |
| Modifier and Type | Method and Description |
|---|---|
java.util.Map<htsjdk.samtools.SAMReadGroupRecord,Fingerprint> |
FingerprintChecker.fingerprintSamFile(java.io.File samFile,
htsjdk.samtools.util.IntervalList loci)
Generates a Fingerprint per read group in the supplied SAM file using the loci provided in
the interval list.
|
java.util.Map<htsjdk.samtools.SAMReadGroupRecord,Fingerprint> |
FingerprintChecker.fingerprintSamFiles(java.util.Collection<java.io.File> files,
int threads,
int waitTime,
java.util.concurrent.TimeUnit waitTimeUnit)
Fingerprints one or more SAM/BAM files at all available loci within the haplotype map, using multiple threads
to speed up the processing.
|
java.util.Map<java.lang.String,Fingerprint> |
FingerprintChecker.identifyContaminant(java.io.File samFile,
double contamination,
int locusMaxReads)
Generates a per-sample Fingerprint for the contaminant in the supplied SAM file.
|
java.util.Map<java.lang.String,Fingerprint> |
FingerprintChecker.loadFingerprints(java.io.File fingerprintFile,
java.lang.String specificSample)
Loads genotypes from the supplied file into one or more Fingerprint objects and returns them in a
Map of Sample->Fingerprint.
|
static java.util.SortedMap<java.lang.String,Fingerprint> |
FingerprintChecker.mergeFingerprintsBySample(java.util.Collection<Fingerprint> inputs)
Takes a collection of fingerprints and, assuming that they are independent, merged the fingerprints
by samples and totals up the probabilities.
|
| Modifier and Type | Method and Description |
|---|---|
static MatchResults |
FingerprintChecker.calculateMatchResults(Fingerprint observedFp,
Fingerprint expectedFp)
Compares two fingerprints and calculates a MatchResults object which contains detailed
information about the match (or mismatch) between fingerprints including the LOD score
for whether or not the two are likely from the same sample.
|
static MatchResults |
FingerprintChecker.calculateMatchResults(Fingerprint observedFp,
Fingerprint expectedFp,
double minPExpected,
double pLoH)
Compares two fingerprints and calculates a MatchResults object which contains detailed
information about the match (or mismatch) between fingerprints including the LOD score
for whether or not the two are likely from the same sample.
|
void |
Fingerprint.merge(Fingerprint other)
Merges the likelihoods from the supplied Fingerprint into the likelihoods for this fingerprint.
|
| Modifier and Type | Method and Description |
|---|---|
htsjdk.samtools.util.IntervalList |
FingerprintChecker.getLociToGenotype(java.util.Collection<Fingerprint> fingerprints)
Takes a set of fingerprints and returns an IntervalList containing all the loci that
can be productively examined in sequencing data to compare to one or more of the
fingerprints.
|
static java.util.SortedMap<java.lang.String,Fingerprint> |
FingerprintChecker.mergeFingerprintsBySample(java.util.Collection<Fingerprint> inputs)
Takes a collection of fingerprints and, assuming that they are independent, merged the fingerprints
by samples and totals up the probabilities.
|