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

We now do lazy loading for the genotype data in VCF. Practically, almost all walkers end of loading the genotype data because we need to be smarter about transfering the unparsed genotype string when modifying VariantContexts; however, this does solve the problem for VR's piece to generate clusters (shaved off 75% of runtime for Ryan's large case). That further optimization will happen later. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4279 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-09-15 00:18:17 +00:00
parent 74d4f124b1
commit 4e83ba411f
2 changed files with 6 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestVariantContextWalker.java
View File

@ -77,6 +77,10 @@ public class TestVariantContextWalker extends RodWalker<Integer, Integer> {
int n = 0;
for (VariantContext vc : tracker.getAllVariantContexts(ref, allowedTypes, context.getLocation(), onlyContextsStartinAtCurrentPosition, takeFirstOnly) ) {
// we need to trigger decoding of the genotype string to pass integration tests
vc.getGenotypes();
if ( writer != null && n == 0 ) {
if ( ! wroteHeader ) {
writer.writeHeader(VariantContextAdaptors.createVCFHeader(null, vc));

4
java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
View File

@ -44,7 +44,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
public void testVariantRecalibrator() {
HashMap<String, List<String>> e = new HashMap<String, List<String>>();
e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf",
Arrays.asList("e7dc06c6d4d8c2cdd03bfdac483aa92b", "038c31c5bb46a4df89b8ee69ec740812","7d42bbdfb69fdfb18cbda13a63d92602")); // Each test checks the md5 of three output files
Arrays.asList("9e4509be067284eefc31e91378faba6a", "038c31c5bb46a4df89b8ee69ec740812","7d42bbdfb69fdfb18cbda13a63d92602")); // Each test checks the md5 of three output files
e.put( validationDataLocation + "lowpass.N3.chr1.raw.vcf",
Arrays.asList("80243bd6731f6b0341fa1762c095a72e", "661360e85392af9c97e386399871854a","371e5a70a4006420737c5ab259e0e23e")); // Each test checks the md5 of three output files
@ -83,7 +83,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testApplyVariantCuts() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "ee22087a813aadf7d9426cab5a6a2164" );
e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "5fc641e291ad7330985ad94d4a347511" );
e.put( validationDataLocation + "lowpass.N3.chr1.raw.vcf", "d9e00e6fe8269b3218880d2c084804c6" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {