zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

BTTJ is now correct. What a terrible waste of time, turns out I'd just reversed the header. Because of this the MD5 had to be updated in the tests. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1910 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2009-10-26 19:24:18 +00:00
parent 24c7f694e6
commit 62c1001790
2 changed files with 20 additions and 11 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
View File

@ -171,6 +171,7 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<Bas
public Set<BaseTransitionTable> updateTables ( Set<BaseTransitionTable> tables, SAMRecord read, int offset, ReferenceContext ref, ReadBackedPileup pileup ) {
List<Comparable> readConditions = buildConditions(read,offset,ref, pileup);
// System.out.println("Updating table with pileup: "+pileup.getBases()+ ( read.getReadNegativeStrandFlag() ? "-" : "+" ) + " Quality: "+read.getBaseQualities()[offset] + " MapQ: "+read.getMappingQuality());
if ( tables == null ) {
tables = new TreeSet<BaseTransitionTable>();
@ -257,7 +258,7 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<Bas
}
public String createHeaderFromConditions() {
String header = "True_base\tObserved_base";
String header = "Observed_base\tTrue_base";
if ( nPreviousBases > 0) {
header = header+"\tPrevious_"+nPreviousBases+"_bases";
@ -327,7 +328,7 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<Bas
Pair<List<GenotypeCall>, GenotypeMetaData> calls = ug.map(tracker,ref,context);
if (calls == null)
return false;
return (! calls.first.get(0).isVariant()) && calls.first.get(0).getNegLog10PError() >= confidentRefThreshold && BaseUtils.isRegularBase(ref.getBase());
return (! calls.first.get(0).isVariant()) && calls.first.get(0).getNegLog10PError() > confidentRefThreshold && BaseUtils.isRegularBase(ref.getBase());
}
@ -422,6 +423,7 @@ class BaseTransitionTable implements Comparable {
//if ( observedBase == refBase ) {
// throw new StingException("BaseTransitionTable received equal observed and reference bases, which should not happen.");
//}
// System.out.println("Table updating: Observed Base: "+observedBase+" Ref base: "+refBase);
table[BaseUtils.simpleBaseToBaseIndex(observedBase)][BaseUtils.simpleBaseToBaseIndex(refBase)]++;
}

25
java/test/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaIntegrationTest.java
View File

@ -13,15 +13,15 @@ import java.util.Arrays;
* To change this template use File | Settings | File Templates.
*/
public class BaseTransitionTableCalculatorJavaIntegrationTest extends WalkerTest{
// MD5s last computed 10/21 at revision 1897
public static final String OUTPUT_MD5_STANDARD = "e88f010ea842bcdb6503a4da24b90edc";
public static final String OUTPUT_MD5_3MISMATCHES = "46f9aadbfe260a286fb6c8cac137dddd";
public static final String OUTPUT_MD5_LOWMAPPINGQUALITY = "0b7447e0a271ffa5c8ff1719db3585e6";
public static final String OUTPUT_MD5_LOWQUALITYSCORE = "87d793f751328b0a9299a69b99cd0112";
public static final String OUTPUT_MD5_LOWCONFIDENTREFTHRESHOLD = "bc70acf997295a6cc13f3e88b254cc24";
public static final String OUTPUT_MD5_HIGHCONFIDENTREFTHRESHOLD = "17d49c12fc64926a71bc32ac1eec7f68";
public static final String OUTPUT_MD5_ALLARGUMENTS = "5599a4a577927fb9875adc26140dee7e";
public static final String OUTPUT_MD5_USEREADGROUP = "f6e8bd2101316deae93512dd09a69567";
// MD5s last computed 10/26 at revision 1897
public static final String OUTPUT_MD5_STANDARD = "bb7f7c8b71a2a19dbbd47699708816b0";
public static final String OUTPUT_MD5_3MISMATCHES = "000bd16dfea8df415e2104fe894aec83";
public static final String OUTPUT_MD5_LOWMAPPINGQUALITY = "db3af69e61e90c59a3ca0ca25605fa67";
public static final String OUTPUT_MD5_LOWQUALITYSCORE = "f990bd4ba5a951b16603131906b74326";
public static final String OUTPUT_MD5_LOWCONFIDENTREFTHRESHOLD = "7c6c2ed2110ee3030fcd060346623fcc";
public static final String OUTPUT_MD5_HIGHCONFIDENTREFTHRESHOLD = "b30efed02e8f6b356e56e5875db40f2c";
public static final String OUTPUT_MD5_ALLARGUMENTS = "3f1901a40e79300da4cbab1488c4839d";
public static final String OUTPUT_MD5_USEREADGROUP = "7422ea018b8dea52398b81502cbe5c38";
public static final String LOCUS = "1:10,000,000-10,200,000";
public static final String BAM_FILE = "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam";
public static final String REFERENCE = "/broad/1KG/reference/human_b36_both.fasta";
@ -33,6 +33,13 @@ public class BaseTransitionTableCalculatorJavaIntegrationTest extends WalkerTest
executeTest("testBaseTransitionTableCalculatorJava", spec);
}
@Test
public void testBaseTransitionTableCalculatorJavaTreeReduce() {
String args = "-T BaseTransitionTableCalculatorJava -of %s -I "+BAM_FILE+" -L "+LOCUS+" -R "+REFERENCE+" -nt 5";
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(args,1,Arrays.asList(OUTPUT_MD5_STANDARD));
executeTest("testBaseTransitionTableCalculatorJava: tree reduce", spec);
}
@Test
public void testBaseTransitionTableCalculatorJavaAdditionalMismatches() {
String args = "-T BaseTransitionTableCalculatorJava -o %s -I "+BAM_FILE+" -L "+LOCUS+" -R "+REFERENCE+" --maxNumMismatches 3";