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Fixed Queue's tagging of RodBindings. 

Fixed argument definition names.
This commit is contained in:
Khalid Shakir 2011-08-21 02:34:20 -04:00
parent 249614e6bb
commit 22ca44c015
1 changed files with 55 additions and 28 deletions
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83
public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
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@ -144,6 +144,9 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
} else if ("input_file".equals(argumentDefinition.fullName) && argumentDefinition.ioType == ArgumentIOType.INPUT) {
return Arrays.asList(new InputTaggedFileDefinitionField(argumentDefinition), new InputIndexesArgumentField(argumentDefinition, BAMIndex.BAMIndexSuffix, ".bam"));
} else if ((RodBinding.class.equals(argumentDefinition.argumentType) || RodBinding.class.equals(argumentDefinition.componentType)) && argumentDefinition.ioType == ArgumentIOType.INPUT) {
return Arrays.asList(new InputTaggedFileDefinitionField(argumentDefinition), new InputIndexesArgumentField(argumentDefinition, Tribble.STANDARD_INDEX_EXTENSION));
} else if (argumentDefinition.ioType == ArgumentIOType.INPUT) {
return Collections.singletonList(new InputArgumentField(argumentDefinition));
@ -196,7 +199,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
}
// if (intervalFields.contains(argumentDefinition.fullName) && argumentDefinition.ioType == ArgumentIOType.INPUT)
// Change intervals exclusize of intervalsString.
// Change intervals exclusive of intervalsString.
private static class IntervalFileArgumentField extends InputArgumentField {
public IntervalFileArgumentField(ArgumentDefinition argumentDefinition) {
super(argumentDefinition);
@ -332,9 +335,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
}
}
/**
* The other extreme of a NamedRodBindingField, allows the user to specify the track name, track type, and the file.
*/
// Allows the user to specify the track name, track type, and the file.
public static class RodBindArgumentField extends ArgumentDefinitionField {
public RodBindArgumentField(ArgumentDefinition argumentDefinition) {
super(argumentDefinition);
@ -347,25 +348,28 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
}
}
/**
* Named input_files.
*/
// Tagged input_files or other rods.
public static class InputTaggedFileDefinitionField extends ArgumentDefinitionField {
public InputTaggedFileDefinitionField(ArgumentDefinition argumentDefinition) {
super(argumentDefinition);
}
@Override protected Class<?> getInnerType() { return null; } // TaggedFile does not need to be imported.
@Override protected String getFieldType() { return "List[File]"; }
@Override protected String getDefaultValue() { return "Nil"; }
@Override protected String getFieldType() { return argumentDefinition.isMultiValued ? "List[File]" : "File"; }
@Override protected String getDefaultValue() { return argumentDefinition.isMultiValued ? "Nil" : "_"; }
@Override protected String getCommandLineTemplate() {
return " + repeat(\"\", %3$s, format=TaggedFile.formatCommandLine(\"%1$s\"))";
if (argumentDefinition.isMultiValued) {
return " + repeat(\"\", %3$s, format=TaggedFile.formatCommandLine(\"%1$s\"))";
} else if (!argumentDefinition.required) {
return " + optional(\"\", %3$s, format=TaggedFile.formatCommandLine(\"%1$s\"))";
} else {
return " + TaggedFile.formatCommandLine(\"%1$s\")(\"\", %3$s, \"\")";
}
}
}
/**
* Adds optional inputs for the indexes of any bams or sams added to this function.
*/
// Adds optional inputs for the indexes of any rods added to this function.
private static class InputIndexesArgumentField extends ArgumentField {
private final boolean originalIsMultiValued;
private final String indexFieldName;
private final String originalFieldName;
private final String indexSuffix;
@ -374,14 +378,19 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
this(originalArgumentDefinition, indexSuffix, null);
}
public InputIndexesArgumentField(ArgumentDefinition originalArgumentDefinition, String indexSuffix, String originalSuffix) {
this.indexFieldName = originalArgumentDefinition.fullName + "Indexes";
this.originalIsMultiValued = originalArgumentDefinition.isMultiValued;
this.indexFieldName = originalArgumentDefinition.fullName + "Index" + (originalIsMultiValued ? "es" : "");
this.originalFieldName = originalArgumentDefinition.fullName;
this.indexSuffix = indexSuffix;
this.originalSuffix = originalSuffix;
}
@Override protected Class<? extends Annotation> getAnnotationIOClass() { return Input.class; }
@Override public String getCommandLineAddition() { return ""; }
@Override protected String getDoc() { return "Dependencies on any indexes of " + this.originalFieldName; }
@Override protected String getDoc() {
return originalIsMultiValued
? "Dependencies on any indexes of " + this.originalFieldName
: "Dependencies on the index of " + this.originalFieldName;
}
@Override protected String getFullName() { return this.indexFieldName; }
@Override protected boolean isRequired() { return false; }
@Override protected String getFieldType() { return "List[File]"; }
@ -389,24 +398,41 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
@Override protected Class<?> getInnerType() { return File.class; }
@Override protected String getRawFieldName() { return this.indexFieldName; }
@Override protected String getFreezeFields() {
if (originalSuffix == null) {
return String.format(
("%1$s ++= %2$s" +
".filter(orig => orig != null)" +
".map(orig => new File(orig.getPath + \"%3$s\"))%n"),
indexFieldName, originalFieldName, indexSuffix);
if (originalIsMultiValued) {
if (originalSuffix == null) {
return String.format(
("%1$s ++= %2$s" +
".filter(orig => orig != null)" +
".map(orig => new File(orig.getPath + \"%3$s\"))%n"),
indexFieldName, originalFieldName, indexSuffix);
} else {
return String.format(
("%1$s ++= %2$s" +
".filter(orig => orig != null && orig.getName.endsWith(\"%4$s\"))" +
".flatMap(orig => Array(" +
" new File(orig.getPath + \"%3$s\")," +
" new File(orig.getPath.stripSuffix(\"%4$s\") + \"%3$s\") ))%n"),
indexFieldName, originalFieldName, indexSuffix, originalSuffix);
}
} else {
return String.format(
("%1$s ++= %2$s" +
".filter(orig => orig != null && orig.getName.endsWith(\"%4$s\"))" +
".flatMap(orig => Array(" +
" new File(orig.getPath + \"%3$s\")," +
" new File(orig.getPath.stripSuffix(\"%4$s\") + \"%3$s\") ))%n"),
indexFieldName, originalFieldName, indexSuffix, originalSuffix);
if (originalSuffix == null) {
return String.format(
("if (%2$s != null)%n " +
"%1$s :+= new File(%2$s.getPath + \"%3$s\")%n"),
indexFieldName, originalFieldName, indexSuffix);
} else {
return String.format(
("if (%2$s != null && %2$s.getName.endsWith(\"%4$s\"))%n " +
"%1$s ++= Array(" +
" new File(%2$s.getPath + \"%3$s\")," +
" new File(%2$s.getPath.stripSuffix(\"%4$s\") + \"%3$s\") )%n"),
indexFieldName, originalFieldName, indexSuffix, originalSuffix);
}
}
}
}
// Tracks an automatically generated index
private static abstract class OutputIndexArgumentField extends ArgumentField {
protected final String indexFieldName;
protected final String originalFieldName;
@ -456,6 +482,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
}
}
// Allows setting the format for floats and doubles
private static class FormatterArgumentField extends ArgumentField {
private final ArgumentField argumentField;
public FormatterArgumentField(ArgumentField argumentField) {