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Update picard to work with new samtools. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@123 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-03-20 21:51:26 +00:00
parent 5dca560c3c
commit 1fcf4c0cbf
5 changed files with 4 additions and 4 deletions
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2
core/java/src/org/broadinstitute/sting/utils/Utils.java
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@ -202,7 +202,7 @@ public class Utils {
} }
public static boolean setupRefContigOrdering(final ReferenceSequenceFile refFile) { public static boolean setupRefContigOrdering(final ReferenceSequenceFile refFile) {
List<SAMSequenceRecord> refContigs = refFile.getSequenceDictionary(); List<SAMSequenceRecord> refContigs = refFile.getSequenceDictionary().getSequences();
HashMap<String, Integer> refContigOrdering = new HashMap<String, Integer>(); HashMap<String, Integer> refContigOrdering = new HashMap<String, Integer>();
if ( refContigs != null ) { if ( refContigs != null ) {

2
ivy.xml
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@ -3,7 +3,7 @@
<dependencies> <dependencies>
<dependency org="net.sf" name="functionalj" rev="latest.integration" /> <dependency org="net.sf" name="functionalj" rev="latest.integration" />
<dependency org="net.sf" name="sam" rev="latest.integration" /> <dependency org="net.sf" name="sam" rev="latest.integration" />
<dependency org="edu.mit.broad" name="picard" rev="200903161458" /> <dependency org="edu.mit.broad" name="picard" rev="200903201733" />
<dependency org="junit" name="junit" rev="4.4" /> <dependency org="junit" name="junit" rev="4.4" />
<dependency org="log4j" name="log4j" rev="1.2.15" /> <dependency org="log4j" name="log4j" rev="1.2.15" />
<dependency org="colt" name="colt" rev="1.2.0" /> <dependency org="colt" name="colt" rev="1.2.0" />

2
playground/java/src/org/broadinstitute/sting/gatk/PrepareROD.java
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@ -47,7 +47,7 @@ public class PrepareROD extends CommandLineProgram {
// Prepare the sort ordering w.r.t. the sequence dictionary // Prepare the sort ordering w.r.t. the sequence dictionary
final ReferenceSequenceFile refFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(REF_FILE_ARG); final ReferenceSequenceFile refFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(REF_FILE_ARG);
List<SAMSequenceRecord> refContigs = refFile.getSequenceDictionary(); List<SAMSequenceRecord> refContigs = refFile.getSequenceDictionary().getSequences();
HashMap<String, Integer> refContigOrdering = new HashMap<String, Integer>(); HashMap<String, Integer> refContigOrdering = new HashMap<String, Integer>();
int i = 0; int i = 0;

BIN
settings/repository/edu.mit.broad/picard-200903161458.jar → settings/repository/edu.mit.broad/picard-200903201733.jar
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2
settings/repository/edu.mit.broad/picard-200903161458.xml → settings/repository/edu.mit.broad/picard-200903201733.xml
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@ -1,3 +1,3 @@
<ivy-module version="1.0"> <ivy-module version="1.0">
<info organisation="edu.mit.broad" module="picard" revision="200903161458" status="integration" publication="20090316145800" /> <info organisation="edu.mit.broad" module="picard" revision="200903201733" status="integration" publication="20090320173300" />
</ivy-module> </ivy-module>