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The SAM spec has now officially reserved my new tags for original cigar and original alignment start... except that OS has been named OP ('original POS') 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3800 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-07-16 00:09:36 +00:00
parent 81eef0d993
commit e7e58d7129
2 changed files with 5 additions and 5 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
View File

@ -58,7 +58,7 @@ import java.util.*;
public class IndelRealigner extends ReadWalker<Integer, Integer> {
public static final String ORIGINAL_CIGAR_TAG = "OC";
public static final String ORIGINAL_START_TAG = "OS";
public static final String ORIGINAL_POSITION_TAG = "OP";
public static final String PROGRAM_RECORD_NAME = "GATK IndelRealigner";
@Argument(fullName="targetIntervals", shortName="targetIntervals", doc="intervals file output from RealignerTargetCreator", required=true)
@ -1179,7 +1179,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
if ( !NO_ORIGINAL_ALIGNMENT_TAGS ) {
read.setAttribute(ORIGINAL_CIGAR_TAG, read.getCigar().toString());
if ( newStart != read.getAlignmentStart() )
read.setAttribute(ORIGINAL_START_TAG, read.getAlignmentStart());
read.setAttribute(ORIGINAL_POSITION_TAG, read.getAlignmentStart());
}
// if it's a paired end read, we need to update the insert size

6
java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
View File

@ -9,7 +9,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
@Test
public void testRealignerLod5() {
String[] md5s = {"ce789182974609da27f3eadbbbcd98c4", "18fca887d1eb7dc300e717ae03b9da62"};
String[] md5s = {"9247b1437ec3b9bc96590524f245220c", "18fca887d1eb7dc300e717ae03b9da62"};
WalkerTestSpec spec = new WalkerTestSpec(
"-T IndelRealigner -noPG -LOD 5 -maxConsensuses 100 -greedy 100 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe",
2,
@ -19,7 +19,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
@Test
public void testRealignerLod50() {
String[] md5s = {"ce789182974609da27f3eadbbbcd98c4", "9537e4f195ce5840136f60fb61201369"};
String[] md5s = {"9247b1437ec3b9bc96590524f245220c", "9537e4f195ce5840136f60fb61201369"};
WalkerTestSpec spec = new WalkerTestSpec(
"-T IndelRealigner -noPG -LOD 50 -maxConsensuses 100 -greedy 100 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe",
2,
@ -29,7 +29,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
@Test
public void testRealignerKnownsOnly() {
String[] md5s = {"f50b9bddd78ed6fb820d2cbdfbff8300", "1091436c40d5ba557d85662999cc0c1d"};
String[] md5s = {"7084d4e543bc756730ab306768028530", "1091436c40d5ba557d85662999cc0c1d"};
WalkerTestSpec spec = new WalkerTestSpec(
"-T IndelRealigner -noPG -LOD 1.0 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10076000 -compress 1 -targetIntervals " + validationDataLocation + "NA12878.indels.intervals -B knownIndels,VCF," + validationDataLocation + "NA12878.indels.vcf -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe -knownsOnly",
2,