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Support for sample sets in AssignSomaticStatus 

-- Also cleaned up SampleUtils.getSamplesFromCommandLine() to return a set, not a list, and trim the sample names.
This commit is contained in:
Mark DePristo 2011-09-19 11:40:45 -04:00
parent 41ffb25b74
commit 3e93f246f7
1 changed files with 15 additions and 4 deletions
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19
public/java/src/org/broadinstitute/sting/utils/SampleUtils.java
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@ -190,11 +190,21 @@ public class SampleUtils {
} }
public static List<String> getSamplesFromCommandLineInput(Collection<String> sampleArgs) { /**
* Returns a new set of samples, containing a final list of samples expanded from sampleArgs
*
* Each element E of sampleArgs can either be a literal sample name or a file. For each E,
* we try to read a file named E from disk, and if possible all lines from that file are expanded
* into unique sample names.
*
* @param sampleArgs
* @return
*/
public static Set<String> getSamplesFromCommandLineInput(Collection<String> sampleArgs) {
if (sampleArgs != null) { if (sampleArgs != null) {
// Let's first go through the list and see if we were given any files. We'll add every entry in the file to our // Let's first go through the list and see if we were given any files. We'll add every entry in the file to our
// sample list set, and treat the entries as if they had been specified on the command line. // sample list set, and treat the entries as if they had been specified on the command line.
List<String> samplesFromFiles = new ArrayList<String>(); Set<String> samplesFromFiles = new HashSet<String>();
for (String SAMPLE_EXPRESSION : sampleArgs) { for (String SAMPLE_EXPRESSION : sampleArgs) {
File sampleFile = new File(SAMPLE_EXPRESSION); File sampleFile = new File(SAMPLE_EXPRESSION);
@ -203,7 +213,7 @@ public class SampleUtils {
List<String> lines = reader.readLines(); List<String> lines = reader.readLines();
for (String line : lines) { for (String line : lines) {
samplesFromFiles.add(line); samplesFromFiles.add(line.trim());
} }
} catch (FileNotFoundException e) { } catch (FileNotFoundException e) {
samplesFromFiles.add(SAMPLE_EXPRESSION); // not a file, so must be a sample samplesFromFiles.add(SAMPLE_EXPRESSION); // not a file, so must be a sample
@ -212,7 +222,8 @@ public class SampleUtils {
return samplesFromFiles; return samplesFromFiles;
} }
return new ArrayList<String>();
return new HashSet<String>();
} }
public static Set<String> getSamplesFromCommandLineInput(Collection<String> vcfSamples, Collection<String> sampleExpressions) { public static Set<String> getSamplesFromCommandLineInput(Collection<String> vcfSamples, Collection<String> sampleExpressions) {