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Cycle covariate now works with pacbio reads. No need to override the platform anymore. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5210 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-02-07 17:14:55 +00:00
parent 2a04e0d378
commit 1fbfd4082e
1 changed files with 2 additions and 1 deletions
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3
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java
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@ -160,6 +160,7 @@ public class CycleCovariate implements StandardCovariate {
*/ */
// todo -- this should be put into a common place in the code base // todo -- this should be put into a common place in the code base
private static List<String> PACBIO_NAMES = Arrays.asList("PACBIO");
private static List<String> ILLUMINA_NAMES = Arrays.asList("ILLUMINA", "SLX", "SOLEXA"); private static List<String> ILLUMINA_NAMES = Arrays.asList("ILLUMINA", "SLX", "SOLEXA");
private static List<String> SOLID_NAMES = Arrays.asList("SOLID"); private static List<String> SOLID_NAMES = Arrays.asList("SOLID");
private static List<String> LS454_NAMES = Arrays.asList("454"); private static List<String> LS454_NAMES = Arrays.asList("454");
@ -180,7 +181,7 @@ public class CycleCovariate implements StandardCovariate {
//----------------------------- //-----------------------------
if( isPlatform(read, ILLUMINA_NAMES) || isPlatform(read, SOLID_NAMES) ) { if( isPlatform(read, ILLUMINA_NAMES) || isPlatform(read, SOLID_NAMES) || isPlatform(read, PACBIO_NAMES)) {
final int init; final int init;
final int increment; final int increment;
if( !read.getReadNegativeStrandFlag() ) { if( !read.getReadNegativeStrandFlag() ) {