zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Vastly better Tribble help message 

Here's a new example:
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 1.1-520-g76495cd):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: Invalid command line: Failed to parse value /humgen/gsa-hpprojects/GATK/data/refGene_b37.filtered.sorted.txt for argument refSeqRodBinding. Message: Invalid command line: No tribble type was provided on the command line and the type of the file could not be determined dynamically. Please add an explicit type tag :TYPE listing the correct type from among the supported types:
##### ERROR        Name        FeatureType   Documentation
##### ERROR      BEAGLE      BeagleFeature   http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_beagle_BeagleCodec.html
##### ERROR         BED         BEDFeature   http://www.broadinstitute.org/gsa/gatkdocs/release/org_broad_tribble_bed_BEDCodec.html
##### ERROR    BEDTABLE       TableFeature   http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_table_BedTableCodec.html
##### ERROR       CGVAR     VariantContext   http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_completegenomics_CGVarCodec.html
##### ERROR       DBSNP       DbSNPFeature   http://www.broadinstitute.org/gsa/gatkdocs/release/org_broad_tribble_dbsnp_DbSNPCodec.html
##### ERROR    GELITEXT    GeliTextFeature   http://www.broadinstitute.org/gsa/gatkdocs/release/org_broad_tribble_gelitext_GeliTextCodec.html
##### ERROR         MAF         MafFeature   http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_gatk_features_maf_MafCodec.html
##### ERROR MILLSDEVINE     VariantContext   http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_MillsDevineCodec.html
##### ERROR   RAWHAPMAP   RawHapMapFeature   http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_hapmap_RawHapMapCodec.html
##### ERROR      REFSEQ      RefSeqFeature   http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_refseq_RefSeqCodec.html
##### ERROR   SAMPILEUP   SAMPileupFeature   http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_sampileup_SAMPileupCodec.html
##### ERROR     SAMREAD     SAMReadFeature   http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_samread_SAMReadCodec.html
##### ERROR      SNPEFF      SnpEffFeature   http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_snpEff_SnpEffCodec.html
##### ERROR     SOAPSNP     VariantContext   http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_soapsnp_SoapSNPCodec.html
##### ERROR       TABLE       TableFeature   http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_table_TableCodec.html
##### ERROR         VCF     VariantContext   http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_vcf_VCFCodec.html
##### ERROR        VCF3     VariantContext   http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_vcf_VCF3Codec.html
##### ERROR ------------------------------------------------------------------------------------------
This commit is contained in:
Mark DePristo 2011-08-18 10:31:32 -04:00
parent c2287c93d7
commit 2d41ba15a4
5 changed files with 42 additions and 13 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
View File

@ -376,7 +376,7 @@ class RodBindingArgumentTypeDescriptor extends ArgumentTypeDescriptor {
} else {
throw new UserException.CommandLineException(
String.format("No tribble type was provided on the command line and the type of the file could not be determined dynamically. " +
"Please add an explicit type tag :TYPE listing the correct type from among the supported types: %s",
"Please add an explicit type tag :TYPE listing the correct type from among the supported types:%n%s",
manager.userFriendlyListOfAvailableFeatures()));
}
}

5
public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
View File

@ -31,6 +31,7 @@ import org.broadinstitute.sting.commandline.ArgumentCollection;
import org.broadinstitute.sting.commandline.CommandLineProgram;
import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
import org.broadinstitute.sting.gatk.filters.ReadFilter;
import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
import org.broadinstitute.sting.gatk.walkers.Attribution;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.exceptions.UserException;
@ -174,6 +175,10 @@ public class CommandLineGATK extends CommandLineExecutable {
StringBuilder additionalHelp = new StringBuilder();
Formatter formatter = new Formatter(additionalHelp);
formatter.format("Available Reference Ordered Data types:%n");
formatter.format(new FeatureManager().userFriendlyListOfAvailableFeatures());
formatter.format("%n");
formatter.format("For a full description of this walker, see its GATKdocs at:%n");
formatter.format("%s%n", HelpUtils.helpLinksToGATKDocs(walkerType));

40
public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java
View File

@ -36,7 +36,9 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.help.HelpUtils;
import javax.mail.Header;
import java.io.File;
import java.util.*;
@ -50,7 +52,7 @@ import java.util.*;
* @author depristo
*/
public class FeatureManager {
public static class FeatureDescriptor {
public static class FeatureDescriptor implements Comparable<FeatureDescriptor> {
final String name;
final FeatureCodec codec;
@ -62,6 +64,7 @@ public class FeatureManager {
public String getName() {
return name;
}
public String getSimpleFeatureName() { return getFeatureClass().getSimpleName(); }
public FeatureCodec getCodec() {
return codec;
}
@ -70,13 +73,18 @@ public class FeatureManager {
@Override
public String toString() {
return String.format("FeatureDescriptor name=%s codec=%s feature=%s", getName(), getCodecClass().getName(), getFeatureClass().getName());
return String.format("FeatureDescriptor name=%s codec=%s feature=%s",
getName(), getCodecClass().getName(), getFeatureClass().getName());
}
@Override
public int compareTo(FeatureDescriptor o) {
return getName().compareTo(o.getName());
}
}
private final PluginManager<FeatureCodec> pluginManager;
private final Collection<FeatureDescriptor> featureDescriptors = new HashSet<FeatureDescriptor>();
private final Collection<FeatureDescriptor> featureDescriptors = new TreeSet<FeatureDescriptor>();
/**
* Construct a FeatureManager
@ -189,10 +197,26 @@ public class FeatureManager {
*/
@Ensures("result != null")
public String userFriendlyListOfAvailableFeatures() {
List<String> names = new ArrayList<String>();
for ( final FeatureDescriptor descriptor : featureDescriptors )
names.add(descriptor.getName());
return Utils.join(",", names);
final String nameHeader="Name", featureHeader = "FeatureType", docHeader="Documentation";
int maxNameLen = nameHeader.length(), maxFeatureNameLen = featureHeader.length();
for ( final FeatureDescriptor descriptor : featureDescriptors ) {
maxNameLen = Math.max(maxNameLen, descriptor.getName().length());
maxFeatureNameLen = Math.max(maxFeatureNameLen, descriptor.getSimpleFeatureName().length());
}
StringBuilder docs = new StringBuilder();
String format = "%" + maxNameLen + "s %" + maxFeatureNameLen + "s %s%n";
docs.append(String.format(format, nameHeader, featureHeader, docHeader));
for ( final FeatureDescriptor descriptor : featureDescriptors ) {
String oneDoc = String.format(format,
descriptor.getName(),
descriptor.getSimpleFeatureName(),
HelpUtils.helpLinksToGATKDocs(descriptor.getCodecClass()));
docs.append(oneDoc);
}
return docs.toString();
}
/**

6
public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java
View File

@ -86,9 +86,9 @@ public class HelpUtils {
public static String helpLinksToGATKDocs(Class c) {
String classPath = htmlFilenameForClass(c);
StringBuilder b = new StringBuilder();
b.append("release version: ").append(URL_ROOT_FOR_RELEASE_GATKDOCS).append(classPath).append("\n");
b.append("stable version: ").append(URL_ROOT_FOR_STABLE_GATKDOCS).append(classPath).append("\n");
b.append("unstable version: ").append(URL_ROOT_FOR_UNSTABLE_GATKDOCS).append(classPath).append("\n");
b.append(URL_ROOT_FOR_RELEASE_GATKDOCS).append(classPath);
//b.append("stable version: ").append(URL_ROOT_FOR_STABLE_GATKDOCS).append(classPath).append("\n");
//b.append("unstable version: ").append(URL_ROOT_FOR_UNSTABLE_GATKDOCS).append(classPath).append("\n");
return b.toString();
}
}

2
public/java/src/org/broadinstitute/sting/utils/text/ListFileUtils.java
View File

@ -161,7 +161,7 @@ public class ListFileUtils {
if ( ! rodBinding.getType().isAssignableFrom(descriptor.getFeatureClass()) )
throw new UserException.BadArgumentValue(rodBinding.getName(),
String.format("Field %s expected type %s, but the type of the input file provided on the command line was %s producing %s. Please make sure that you have provided the correct file type and/or that you are not binding your rod to a name matching one of the available types.",
rodBinding.getName(), rodBinding.getType(), descriptor.getName(), descriptor.getFeatureClass()));
rodBinding.getName(), rodBinding.getType(), descriptor.getName(), descriptor.getSimpleFeatureName()));
rodBindings.add(triplet);