Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
This commit is contained in:
Guillermo del Angel
commit
c8d3a720f9
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@ -159,10 +159,11 @@ public class CycleCovariate implements StandardCovariate {
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*/
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// todo -- this should be put into a common place in the code base
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private static List<String> PACBIO_NAMES = Arrays.asList("PACBIO");
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private static List<String> ILLUMINA_NAMES = Arrays.asList("ILLUMINA", "SLX", "SOLEXA");
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private static List<String> SOLID_NAMES = Arrays.asList("SOLID");
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private static List<String> LS454_NAMES = Arrays.asList("454");
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private static List<String> COMPLETE_GENOMICS_NAMES = Arrays.asList("COMPLETE");
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private static List<String> PACBIO_NAMES = Arrays.asList("PACBIO");
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private static boolean isPlatform(SAMRecord read, List<String> names) {
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String pl = read.getReadGroup().getPlatform().toUpperCase();
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@ -176,11 +177,10 @@ public class CycleCovariate implements StandardCovariate {
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public void getValues(SAMRecord read, Comparable[] comparable) {
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//-----------------------------
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// ILLUMINA and SOLID
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// Illumina, Solid, PacBio, and Complete Genomics
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//-----------------------------
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if( isPlatform(read, ILLUMINA_NAMES) || isPlatform(read, SOLID_NAMES) || isPlatform(read, PACBIO_NAMES)) {
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if( isPlatform(read, ILLUMINA_NAMES) || isPlatform(read, SOLID_NAMES) || isPlatform(read, PACBIO_NAMES) || isPlatform(read, COMPLETE_GENOMICS_NAMES) ) {
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final int init;
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final int increment;
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if( !read.getReadNegativeStrandFlag() ) {
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@ -222,6 +222,11 @@ public class CycleCovariate implements StandardCovariate {
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cycle += increment;
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}
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}
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//-----------------------------
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// 454
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//-----------------------------
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else if ( isPlatform(read, LS454_NAMES) ) { // Some bams have "LS454" and others have just "454"
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final int readLength = read.getReadLength();
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@ -245,8 +245,7 @@ public class RecalDataManager {
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readGroup.setPlatform( RAC.DEFAULT_PLATFORM );
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((GATKSAMRecord)read).setReadGroup( readGroup );
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} else {
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throw new UserException.MalformedBAM(read, "The input .bam file contains reads with no read group. First observed at read with name = " + read.getReadName() +
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" Users must set both the default read group using the --default_read_group <String> argument and the default platform using the --default_platform <String> argument." );
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throw new UserException.MalformedBAM(read, "The input .bam file contains reads with no read group. First observed at read with name = " + read.getReadName() );
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}
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}
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@ -271,8 +270,7 @@ public class RecalDataManager {
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}
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readGroup.setPlatform( RAC.DEFAULT_PLATFORM );
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} else {
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throw new UserException.MalformedBAM(read, "The input .bam file contains reads with no platform information. First observed at read with name = " + read.getReadName() +
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" Users must set the default platform using the --default_platform <String> argument." );
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throw new UserException.MalformedBAM(read, "The input .bam file contains reads with no platform information. First observed at read with name = " + read.getReadName() );
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}
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}
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}
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@ -26,6 +26,7 @@
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package org.broadinstitute.sting.gatk.walkers.recalibration;
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import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.commandline.Hidden;
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/**
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* Created by IntelliJ IDEA.
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@ -41,22 +42,29 @@ public class RecalibrationArgumentCollection {
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//////////////////////////////////
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// Shared Command Line Arguments
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//////////////////////////////////
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@Hidden
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@Argument(fullName="default_read_group", shortName="dRG", required=false, doc="If a read has no read group then default to the provided String.")
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public String DEFAULT_READ_GROUP = null;
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@Hidden
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@Argument(fullName="default_platform", shortName="dP", required=false, doc="If a read has no platform then default to the provided String. Valid options are illumina, 454, and solid.")
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public String DEFAULT_PLATFORM = null;
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@Hidden
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@Argument(fullName="force_read_group", shortName="fRG", required=false, doc="If provided, the read group ID of EVERY read will be forced to be the provided String. This is useful to collapse all data into a single read group.")
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public String FORCE_READ_GROUP = null;
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@Hidden
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@Argument(fullName="force_platform", shortName="fP", required=false, doc="If provided, the platform of EVERY read will be forced to be the provided String. Valid options are illumina, 454, and solid.")
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public String FORCE_PLATFORM = null;
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@Hidden
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@Argument(fullName = "window_size_nqs", shortName="nqs", doc="The window size used by MinimumNQSCovariate for its calculation", required=false)
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public int WINDOW_SIZE = 5;
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/**
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* This window size tells the module in how big of a neighborhood around the current base it should look for the minimum base quality score.
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*/
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@Hidden
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@Argument(fullName = "homopolymer_nback", shortName="nback", doc="The number of previous bases to look at in HomopolymerCovariate", required=false)
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public int HOMOPOLYMER_NBACK = 7;
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@Hidden
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@Argument(fullName = "exception_if_no_tile", shortName="throwTileException", doc="If provided, TileCovariate will throw an exception when no tile can be found. The default behavior is to use tile = -1", required=false)
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public boolean EXCEPTION_IF_NO_TILE = false;
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@ -0,0 +1,56 @@
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package org.broadinstitute.sting.utils;
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import com.google.java.contract.Ensures;
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import com.google.java.contract.Requires;
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import java.util.Comparator;
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/**
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*
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* @author Mauricio Carneiro
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* @since 9/28/11
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*/
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public class GenomeLocComparator implements Comparator<GenomeLoc> {
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/**
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* compares genomeLoc's contigs
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*
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* @param gl1 the genome loc to compare contigs
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* @param gl2 the genome loc to compare contigs
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* @return 0 if equal, -1 if gl2.contig is greater, 1 if gl1.contig is greater
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*/
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@Requires("gl2 != null")
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@Ensures("result == 0 || result == 1 || result == -1")
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public final int compareContigs( GenomeLoc gl1, GenomeLoc gl2 ) {
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if (gl1.contigIndex == gl2.contigIndex)
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return 0;
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else if (gl1.contigIndex > gl2.contigIndex)
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return 1;
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return -1;
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}
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@Requires("gl2 != null")
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@Ensures("result == 0 || result == 1 || result == -1")
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public int compare ( GenomeLoc gl1, GenomeLoc gl2 ) {
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int result = 0;
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if ( gl1 == gl2 ) {
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result = 0;
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}
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else if(GenomeLoc.isUnmapped(gl1))
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result = 1;
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else if(GenomeLoc.isUnmapped(gl2))
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result = -1;
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else {
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final int cmpContig = compareContigs(gl1, gl2);
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if ( cmpContig != 0 ) {
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result = cmpContig;
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} else {
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if ( gl1.getStart() < gl2.getStart() ) result = -1;
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if ( gl1.getStart() > gl2.getStart() ) result = 1;
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}
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}
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return result;
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}
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}
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@ -93,8 +93,9 @@ public class ReadClipper {
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public SAMRecord hardClipBothEndsByReferenceCoordinates(int left, int right) {
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if (left == right)
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return new SAMRecord(read.getHeader());
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this.read = hardClipByReferenceCoordinates(right, -1);
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return hardClipByReferenceCoordinates(-1, left);
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SAMRecord leftTailRead = hardClipByReferenceCoordinates(right, -1);
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ReadClipper clipper = new ReadClipper(leftTailRead);
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return clipper.hardClipByReferenceCoordinatesLeftTail(left);
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}
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public SAMRecord hardClipLowQualEnds(byte lowQual) {
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@ -893,6 +893,10 @@ public class ReadUtils {
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// base before the deletion (see warning in function contracts)
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else if (fallsInsideDeletion && !endsWithinCigar)
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readBases += shift - 1;
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// If we reached our goal inside a deletion then we must backtrack to the last base before the deletion
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else if (fallsInsideDeletion && endsWithinCigar)
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readBases--;
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}
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}
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