Uses of Class
picard.analysis.SinglePassSamProgram

Packages that use SinglePassSamProgram

Package	Description
picard.analysis
picard.analysis.artifacts

Uses of SinglePassSamProgram in picard.analysis

Subclasses of SinglePassSamProgram in picard.analysis

Modifier and Type	Class and Description
class	CollectAlignmentSummaryMetrics A command line tool to read a BAM file and produce standard alignment metrics that would be applicable to any alignment.
class	CollectBaseDistributionByCycle
class	CollectGcBiasMetrics Tool to collect information about GC bias in the reads in a given BAM file.
class	CollectInsertSizeMetrics Command line program to read non-duplicate insert sizes, create a Histogram and report distribution statistics.
class	CollectQualityYieldMetrics Command line program to calibrate quality yield metrics
class	CollectRnaSeqMetrics
class	MeanQualityByCycle Program to generate a data table and chart of mean quality by cycle from a BAM file.
class	QualityScoreDistribution Charts quality score distribution within a BAM file.

Methods in picard.analysis that return SinglePassSamProgram

Modifier and Type	Method and Description
SinglePassSamProgram	CollectMultipleMetrics.ProgramInterface.makeInstance(java.lang.String outbase, java.lang.String outext, java.io.File input, java.io.File reference, java.util.Set<MetricAccumulationLevel> metricAccumulationLevel, java.io.File dbSnp, java.io.File intervals)

Method parameters in picard.analysis with type arguments of type SinglePassSamProgram

Modifier and Type	Method and Description
static void	SinglePassSamProgram.makeItSo(java.io.File input, java.io.File referenceSequence, boolean assumeSorted, long stopAfter, java.util.Collection<SinglePassSamProgram> programs)

Uses of SinglePassSamProgram in picard.analysis.artifacts

Subclasses of SinglePassSamProgram in picard.analysis.artifacts

Modifier and Type	Class and Description
class	CollectSequencingArtifactMetrics Quantify substitution errors caused by mismatched base pairings during various stages of sample / library prep.