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Fix bugs as reported on the forum: BED needs to be explicitly set as the default output format and the output didn't actually adhere to the BED spec.

This commit is contained in:
Eric Banks 2012-11-08 15:07:47 -05:00
parent 17ab3a39d5
commit e9183d9fe0
2 changed files with 6 additions and 6 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
View File

@ -191,7 +191,7 @@ public class CallableLoci extends LocusWalker<CallableLoci.CallableBaseState, Ca
*/
@Advanced
@Argument(fullName = "format", shortName = "format", doc = "Output format", required = false)
OutputFormat outputFormat;
OutputFormat outputFormat = OutputFormat.BED;
public enum OutputFormat {
/**
@ -297,7 +297,7 @@ public class CallableLoci extends LocusWalker<CallableLoci.CallableBaseState, Ca
}
public String toString() {
return String.format("%s %d %d %s", loc.getContig(), loc.getStart(), loc.getStop(), state);
return String.format("%s\t%d\t%d\t%s", loc.getContig(), loc.getStart()-1, loc.getStop(), state);
}
}

8
public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalkerIntegrationTest.java
View File

@ -38,7 +38,7 @@ public class CallableLociWalkerIntegrationTest extends WalkerTest {
public void testCallableLociWalkerBed() {
String gatk_args = commonArgs + " -format BED -L 1:10,000,000-11,000,000 -summary %s";
WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2,
Arrays.asList("9e4ec9c23f21a8162d27a39ab057398c", SUMMARY_MD5));
Arrays.asList("42e86c06c167246a28bffdacaca75ffb", SUMMARY_MD5));
executeTest("formatBed", spec);
}
@ -46,7 +46,7 @@ public class CallableLociWalkerIntegrationTest extends WalkerTest {
public void testCallableLociWalkerPerBase() {
String gatk_args = commonArgs + " -format STATE_PER_BASE -L 1:10,000,000-11,000,000 -summary %s";
WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2,
Arrays.asList("e6044b4495ef24f542403e6a94437068", SUMMARY_MD5));
Arrays.asList("d66c525d9c70f62df8156261d3e535ad", SUMMARY_MD5));
executeTest("format_state_per_base", spec);
}
@ -54,7 +54,7 @@ public class CallableLociWalkerIntegrationTest extends WalkerTest {
public void testCallableLociWalker2() {
String gatk_args = commonArgs + " -format BED -L 1:10,000,000-10,000,100 -L 1:10,000,110-10,000,120 -summary %s";
WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2,
Arrays.asList("c671f65712d9575b8b3e1f1dbedc146e", "d287510eac04acf5a56f5cde2cba0e4a"));
Arrays.asList("330f476085533db92a9dbdb3a127c041", "d287510eac04acf5a56f5cde2cba0e4a"));
executeTest("formatBed by interval", spec);
}
@ -62,7 +62,7 @@ public class CallableLociWalkerIntegrationTest extends WalkerTest {
public void testCallableLociWalker3() {
String gatk_args = commonArgs + " -format BED -L 1:10,000,000-11,000,000 -minDepth 10 -maxDepth 100 --minBaseQuality 10 --minMappingQuality 20 -summary %s";
WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2,
Arrays.asList("b7d26a470ef906590249f2fa45fd6bdd", "da431d393f7c2b2b3e27556b86c1dbc7"));
Arrays.asList("46a53379aaaf9803276a0a34b234f6ab", "da431d393f7c2b2b3e27556b86c1dbc7"));
executeTest("formatBed lots of arguments", spec);
}
}