org.utgenome.format.sam
Class SAMReader

java.lang.Object
  org.utgenome.format.sam.SAMReader

public class SAMReader
extends Object

SAM File reader

Author:

leo

Nested Class Summary

static class	SAMReader.CompleteSAMReadFactory
static class	SAMReader.LightWeightSAMReadFactory
static interface	SAMReader.SAMReadFactory

Constructor Summary

SAMReader()

Method Summary

static List<OnGenome>	depthCoverage(ChrLoc loc, int pixelWidth, List<net.sf.samtools.SAMRecord> loadedReadSet, net.sf.samtools.util.CloseableIterator<net.sf.samtools.SAMRecord> cursor)
static List<OnGenome>	depthCoverage(File bamFile, ChrLoc loc, int pixelWidth, ReadQueryConfig config)
static List<OnGenome>	depthCoverageInWIG(File wigFile, ChrLoc loc, int pixelWidth, ReadQueryConfig config)
static File	getBamIndexFile(File bamFile)
List<String>	getChrList(File samOrBamFile)
static Iterable<net.sf.samtools.SAMRecord>	getSAMRecordReader(InputStream samFile)
static List<OnGenome>	overlapQuery(File bamFile, ChrLoc loc, int pixelWidth, ReadQueryConfig config) Retrieved SAMReads (or SAMReadPair) overlapped with the specified interval

Methods inherited from class java.lang.Object

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

Constructor Detail

SAMReader

public SAMReader()

Method Detail

getSAMRecordReader

public static Iterable<net.sf.samtools.SAMRecord> getSAMRecordReader(InputStream samFile)

getChrList

public List<String> getChrList(File samOrBamFile)

getBamIndexFile

public static File getBamIndexFile(File bamFile)

depthCoverage

public static List<OnGenome> depthCoverage(ChrLoc loc,
                                           int pixelWidth,
                                           List<net.sf.samtools.SAMRecord> loadedReadSet,
                                           net.sf.samtools.util.CloseableIterator<net.sf.samtools.SAMRecord> cursor)

depthCoverage

public static List<OnGenome> depthCoverage(File bamFile,
                                           ChrLoc loc,
                                           int pixelWidth,
                                           ReadQueryConfig config)
                                    throws UTGBException

Throws:

UTGBException

depthCoverageInWIG

public static List<OnGenome> depthCoverageInWIG(File wigFile,
                                                ChrLoc loc,
                                                int pixelWidth,
                                                ReadQueryConfig config)
                                         throws UTGBException

Throws:

UTGBException

overlapQuery

public static List<OnGenome> overlapQuery(File bamFile,
                                          ChrLoc loc,
                                          int pixelWidth,
                                          ReadQueryConfig config)
                                   throws UTGBException

Retrieved SAMReads (or SAMReadPair) overlapped with the specified interval

Parameters:

bamFile -

loc -

Returns:

Throws:

UTGBException