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Fixing the error messages thrown with bad interval arguments. I simplified the exception handling and made the messages more verbose. 

Note: the -L argument takes both interval strings and filenames. If you specify an interval string that is also a file, an error will be thrown to move the file: ie. if you have a file "chr1" in the parent directory, GATK will ask you to move/delete it. But, this only happens with interval string arguments, NOT with intervals that are contained in files, which is a majority of the use case. 



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3602 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
bthomas 2010-06-21 21:49:41 +00:00
parent 300a18b85f
commit 9d6a341d15
2 changed files with 26 additions and 18 deletions
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14
java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
View File

@ -26,6 +26,7 @@
package org.broadinstitute.sting.utils;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
@ -314,7 +315,7 @@ public class GenomeLocParser {
* 'chr2', 'chr2:1000000' or 'chr2:1,000,000-2,000,000'
*
* @param file_name
* @param rule also merge abutting intervals
* @return List<GenomeLoc> List of Genome Locs that have been parsed from file
*/
public static List<GenomeLoc> intervalFileToList(final String file_name) {
// try to open file
@ -368,22 +369,15 @@ public class GenomeLocParser {
List<GenomeLoc> ret = new ArrayList<GenomeLoc>();
XReadLines reader = new XReadLines(new File(file_name));
for(String line: reader) {
try {
ret.add(parseGenomeInterval(line));
}
catch (Exception e2) {
throw new StingException(String.format("Unable to parse interval: %s in file: %s", line, file_name));
}
}
reader.close();
// always return null instead of empty list
return ret.isEmpty() ? null : ret;
}
catch (Exception e2) {
logger.error("Attempt to parse interval file in GATK format failed: " + e2.getMessage());
e2.printStackTrace();
throw new StingException("Unable to parse out interval file in either format", e);
catch (IOException e2) {
throw new StingException("An I/O error occurred while reading the interval file.", e);
}
}
}

30
java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java
View File

@ -47,8 +47,16 @@ public class IntervalUtils {
for (String fileOrInterval : argument.split(";")) {
// if it's a file, add items to raw interval list
if (isIntervalFile(fileOrInterval))
rawIntervals.addAll(GenomeLocParser.intervalFileToList(fileOrInterval));
if (isIntervalFile(fileOrInterval)) {
try {
rawIntervals.addAll(GenomeLocParser.intervalFileToList(fileOrInterval));
}
catch (Exception e) {
throw new StingException(String.format("Interval file %s could not be parsed in either format. " +
"The problem is:%n%s",
fileOrInterval, e.getMessage()), e);
}
}
// otherwise treat as an interval -> parse and add to raw interval list
else {
@ -88,15 +96,21 @@ public class IntervalUtils {
public static boolean isIntervalFile(String str) {
// should we define list of file extensions as a public array somewhere?
// is regex or endsiwth better?
File file = new File(str);
if (str.toUpperCase().endsWith(".BED") || str.toUpperCase().endsWith(".LIST") ||
str.toUpperCase().endsWith(".PICARD") || str.toUpperCase().endsWith(".INTERVAL_LIST")
|| str.toUpperCase().endsWith(".INTERVALS"))
return true;
|| str.toUpperCase().endsWith(".INTERVALS")) {
if (file.exists())
return true;
else
throw new StingException(String.format("The interval file %s does not exist.", file.getAbsolutePath()));
}
if(new File(str).exists())
throw new StingException("Interval argument looks like a filename, but does not have one of " +
"the supported extensions (.bed, .list, .picard, .interval_list, or .intervals). " +
"Please rename your file with the appropriate extension.");
if(file.exists())
throw new StingException(String.format("The interval file %s does not have one of " +
"the supported extensions (.bed, .list, .picard, .interval_list, or .intervals). " +
"Please rename your file with the appropriate extension. If %s is NOT supposed to be a file, " +
"please move or rename the file at location %s", str, str, file.getAbsolutePath()));
else return false;
}