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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Eric Banks 2011-09-28 13:13:21 -04:00
parent bb619a9a3c 5812004e06
commit 1f0e354fae
2 changed files with 17 additions and 8 deletions
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23
public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
View File

@ -325,11 +325,14 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
return Arrays.toString((Object[])value);
else
throw new RuntimeException("Unexpected array type in prettyPrintValue. Value was " + value + " type is " + type);
} else if ( RodBinding.class.isAssignableFrom(value.getClass() ) )
} else if ( RodBinding.class.isAssignableFrom(value.getClass() ) ) {
// annoying special case to handle the UnBound() constructor
return "none";
return value.toString();
} else if ( value instanceof String ) {
return value.equals("") ? "\"\"" : value;
} else {
return value.toString();
}
}
/**
@ -432,11 +435,17 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
* Returns a Pair of (main, synonym) names for argument with fullName s1 and
* shortName s2. The main is selected to be the longest of the two, provided
* it doesn't exceed MAX_DISPLAY_NAME, in which case the shorter is taken.
* @param s1
* @param s2
* @return
*
* @param s1 the short argument name without -, or null if not provided
* @param s2 the long argument name without --, or null if not provided
* @return A pair of fully qualified names (with - or --) for the argument. The first
* element is the primary display name while the second (potentially null) is a
* synonymous name.
*/
Pair<String, String> displayNames(String s1, String s2) {
s1 = s1 == null ? null : "-" + s1;
s2 = s2 == null ? null : "--" + s2;
if ( s1 == null ) return new Pair<String, String>(s2, null);
if ( s2 == null ) return new Pair<String, String>(s1, null);
@ -510,7 +519,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
*/
protected Map<String, Object> docForArgument(FieldDoc fieldDoc, ArgumentSource source, ArgumentDefinition def) {
Map<String, Object> root = new HashMap<String, Object>();
Pair<String, String> names = displayNames("-" + def.shortName, "--" + def.fullName);
Pair<String, String> names = displayNames(def.shortName, def.fullName);
root.put("name", names.getFirst() );

2
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
View File

@ -825,7 +825,7 @@ public class ReadUtils {
* @return the read coordinate corresponding to the requested reference coordinate. (see warning!)
*/
@Requires({"refCoord >= read.getUnclippedStart()", "refCoord <= read.getUnclippedEnd()"})
@Ensures({"result >= 0", "result < read.getReadLength()"})
@Ensures({"result.getFirst() >= 0", "result.getFirst() < read.getReadLength()"})
public static Pair<Integer, Boolean> getReadCoordinateForReferenceCoordinate(SAMRecord read, int refCoord) {
int readBases = 0;
int refBases = 0;