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Fixed null checkes in ArgumentTypeDescriptor due to ArgumentMatchValue updates. 

Fixed @Arguments such as scatter count that were labeled as java.io.File via incorrect @Input annotation.
This commit is contained in:
Khalid Shakir 2012-10-18 16:57:15 -04:00
parent a4184716d8
commit 403654d40a
2 changed files with 16 additions and 15 deletions
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6
public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
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@ -532,7 +532,7 @@ class SimpleArgumentTypeDescriptor extends ArgumentTypeDescriptor {
Object[] vals = type.getEnumConstants();
Object defaultEnumeration = null; // as we look at options, record the default option if it exists
for (Object val : vals) {
if (String.valueOf(val).equalsIgnoreCase(value.asString())) return val;
if (String.valueOf(val).equalsIgnoreCase(value == null ? null : value.asString())) return val;
try { if (type.getField(val.toString()).isAnnotationPresent(EnumerationArgumentDefault.class)) defaultEnumeration = val; }
catch (NoSuchFieldException e) { throw new ReviewedStingException("parsing " + type.toString() + "doesn't contain the field " + val.toString()); }
}
@ -546,10 +546,10 @@ class SimpleArgumentTypeDescriptor extends ArgumentTypeDescriptor {
else
throw new UnknownEnumeratedValueException(createDefaultArgumentDefinition(source),value.asString());
} else if (type.equals(File.class)) {
result = value.asFile();
result = value == null ? null : value.asFile();
} else {
Constructor ctor = type.getConstructor(String.class);
result = ctor.newInstance(value.asString());
result = ctor.newInstance(value == null ? null : value.asString());
}
} catch (UserException e) {
throw e;

25
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
View File

@ -13,6 +13,7 @@ import net.sf.samtools.SAMFileHeader.SortOrder
import org.broadinstitute.sting.queue.util.QScriptUtils
import org.broadinstitute.sting.queue.function.ListWriterFunction
import org.broadinstitute.sting.commandline.Hidden
import org.broadinstitute.sting.commandline
class DataProcessingPipeline extends QScript {
qscript =>
@ -41,34 +42,34 @@ class DataProcessingPipeline extends QScript {
@Input(doc="The path to the binary of bwa (usually BAM files have already been mapped - but if you want to remap this is the option)", fullName="path_to_bwa", shortName="bwa", required=false)
var bwaPath: File = _
@Input(doc="the project name determines the final output (BAM file) base name. Example NA12878 yields NA12878.processed.bam", fullName="project", shortName="p", required=false)
@Argument(doc="the project name determines the final output (BAM file) base name. Example NA12878 yields NA12878.processed.bam", fullName="project", shortName="p", required=false)
var projectName: String = "project"
@Input(doc="Output path for the processed BAM files.", fullName="output_directory", shortName="outputDir", required=false)
@Argument(doc="Output path for the processed BAM files.", fullName="output_directory", shortName="outputDir", required=false)
var outputDir: String = ""
@Input(doc="the -L interval string to be used by GATK - output bams at interval only", fullName="gatk_interval_string", shortName="L", required=false)
@Argument(doc="the -L interval string to be used by GATK - output bams at interval only", fullName="gatk_interval_string", shortName="L", required=false)
var intervalString: String = ""
@Input(doc="an intervals file to be used by GATK - output bams at intervals only", fullName="gatk_interval_file", shortName="intervals", required=false)
var intervals: File = _
@Input(doc="Cleaning model: KNOWNS_ONLY, USE_READS or USE_SW", fullName="clean_model", shortName="cm", required=false)
@Argument(doc="Cleaning model: KNOWNS_ONLY, USE_READS or USE_SW", fullName="clean_model", shortName="cm", required=false)
var cleaningModel: String = "USE_READS"
@Input(doc="Decompose input BAM file and fully realign it using BWA and assume Single Ended reads", fullName="use_bwa_single_ended", shortName="bwase", required=false)
@Argument(doc="Decompose input BAM file and fully realign it using BWA and assume Single Ended reads", fullName="use_bwa_single_ended", shortName="bwase", required=false)
var useBWAse: Boolean = false
@Input(doc="Decompose input BAM file and fully realign it using BWA and assume Pair Ended reads", fullName="use_bwa_pair_ended", shortName="bwape", required=false)
@Argument(doc="Decompose input BAM file and fully realign it using BWA and assume Pair Ended reads", fullName="use_bwa_pair_ended", shortName="bwape", required=false)
var useBWApe: Boolean = false
@Input(doc="Decompose input BAM file and fully realign it using BWA SW", fullName="use_bwa_sw", shortName="bwasw", required=false)
@Argument(doc="Decompose input BAM file and fully realign it using BWA SW", fullName="use_bwa_sw", shortName="bwasw", required=false)
var useBWAsw: Boolean = false
@Input(doc="Number of threads BWA should use", fullName="bwa_threads", shortName="bt", required=false)
@Argument(doc="Number of threads BWA should use", fullName="bwa_threads", shortName="bt", required=false)
var bwaThreads: Int = 1
@Input(doc="Perform validation on the BAM files", fullName="validation", shortName="vs", required=false)
@Argument(doc="Perform validation on the BAM files", fullName="validation", shortName="vs", required=false)
var validation: Boolean = false
@ -76,15 +77,15 @@ class DataProcessingPipeline extends QScript {
* Hidden Parameters
****************************************************************************/
@Hidden
@Input(doc="How many ways to scatter/gather", fullName="scatter_gather", shortName="sg", required=false)
@Argument(doc="How many ways to scatter/gather", fullName="scatter_gather", shortName="sg", required=false)
var nContigs: Int = -1
@Hidden
@Input(doc="Define the default platform for Count Covariates -- useful for techdev purposes only.", fullName="default_platform", shortName="dp", required=false)
@Argument(doc="Define the default platform for Count Covariates -- useful for techdev purposes only.", fullName="default_platform", shortName="dp", required=false)
var defaultPlatform: String = ""
@Hidden
@Input(doc="Run the pipeline in test mode only", fullName = "test_mode", shortName = "test", required=false)
@Argument(doc="Run the pipeline in test mode only", fullName = "test_mode", shortName = "test", required=false)
var testMode: Boolean = false