org.broadinstitute.hellbender.tools.spark.pathseq

Class PSUtils

java.lang.Object

org.broadinstitute.hellbender.tools.spark.pathseq.PSUtils

public final class PSUtils
extends java.lang.Object

Common functions for PathSeq

Constructor Summary

Constructors

Constructor and Description
PSUtils()

Method Summary

Modifier and Type	Method and Description
static htsjdk.samtools.SAMFileHeader	checkAndClearHeaderSequences(htsjdk.samtools.SAMFileHeader inputHeader, PSFilterArgumentCollection filterArgs, org.apache.logging.log4j.Logger logger) Returns a deep copy of the input header with an empty sequence dictionary, and logs warnings if the input may be aligned but --isHostAligned was not set to true (or vice versa).
static int	getMatchesLessDeletions(htsjdk.samtools.Cigar cigar, int nmTagValue)
static void	logItemizedWarning(org.apache.logging.log4j.Logger logger, java.util.Collection<?> items, java.lang.String warning) Prints warning message followed by a list of relevant items
static java.lang.String[]	parseCommaDelimitedArgList(java.lang.String arg)
static byte[]	parseMask(java.lang.String maskArg, int kSize) Parses command-line option for specifying kmer spacing masks
static int	pathseqGetRecommendedNumReducers(java.lang.String inputPath, int numReducers, int targetPartitionSize) Same as GATKSparkTool's getRecommendedNumReducers(), but can specify input BAM path (for when --input is not used)
static org.apache.spark.api.java.JavaRDD<GATKRead>	primaryReads(org.apache.spark.api.java.JavaRDD<GATKRead> reads)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PSUtils

public PSUtils()

Method Detail

primaryReads

public static org.apache.spark.api.java.JavaRDD<GATKRead> primaryReads(org.apache.spark.api.java.JavaRDD<GATKRead> reads)

parseCommaDelimitedArgList

public static java.lang.String[] parseCommaDelimitedArgList(java.lang.String arg)

parseMask

public static byte[] parseMask(java.lang.String maskArg,
                               int kSize)

Parses command-line option for specifying kmer spacing masks

logItemizedWarning

public static void logItemizedWarning(org.apache.logging.log4j.Logger logger,
                                      java.util.Collection<?> items,
                                      java.lang.String warning)

Prints warning message followed by a list of relevant items

pathseqGetRecommendedNumReducers

public static int pathseqGetRecommendedNumReducers(java.lang.String inputPath,
                                                   int numReducers,
                                                   int targetPartitionSize)

Same as GATKSparkTool's getRecommendedNumReducers(), but can specify input BAM path (for when --input is not used)

checkAndClearHeaderSequences

public static htsjdk.samtools.SAMFileHeader checkAndClearHeaderSequences(htsjdk.samtools.SAMFileHeader inputHeader,
                                                                         PSFilterArgumentCollection filterArgs,
                                                                         org.apache.logging.log4j.Logger logger)

Returns a deep copy of the input header with an empty sequence dictionary, and logs warnings if the input may be aligned but --isHostAligned was not set to true (or vice versa).

getMatchesLessDeletions

public static int getMatchesLessDeletions(htsjdk.samtools.Cigar cigar,
                                          int nmTagValue)