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<GenomeRange>	depthCoverage(ChrLoc loc, int pixelWidth, List<net.sf.samtools.SAMRecord> loadedReadSet, net.sf.samtools.util.CloseableIterator<net.sf.samtools.SAMRecord> cursor)
static List<GenomeRange>	depthCoverage(File bamFile, ChrLoc loc, int pixelWidth, ReadQueryConfig config)
static List<GenomeRange>	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<GenomeRange>	overlapQuery(File bamFile, ChrLoc loc, int pixelWidth, ReadQueryConfig config) Retrieved SAMReads (or SAMReadPair) overlapped with the specified interval
static String	trimPairedEndSuffix(String readName) Trim /1, /2 suffixes

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<GenomeRange> 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<GenomeRange> depthCoverage(File bamFile,
                                              ChrLoc loc,
                                              int pixelWidth,
                                              ReadQueryConfig config)
                                       throws UTGBException

Throws:

UTGBException

depthCoverageInWIG

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

Throws:

UTGBException

overlapQuery

public static List<GenomeRange> 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

trimPairedEndSuffix

public static String trimPairedEndSuffix(String readName)

Trim /1, /2 suffixes

Parameters:

readNam -

Returns: