Simple change to allow a list of samples or regular expressions to be provided in a text file (one line per sample).

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4074 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java

@@ -40,6 +40,8 @@ import org.broadinstitute.sting.gatk.walkers.RMD;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.SampleUtils;
+import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.text.XReadLines;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFWriterImpl;
@@ -47,6 +49,8 @@ import org.broadinstitute.sting.utils.genotype.vcf.VCFWriterImpl;
 import java.util.*;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
+import java.io.File;
+import java.io.FileNotFoundException;
 
 /**
  * Takes a VCF file, selects variants based on sample(s) in which it was found and/or on various annotation criteria,
@@ -54,7 +58,7 @@ import java.util.regex.Pattern;
  */
 @Requires(value={},referenceMetaData=@RMD(name="variant", type=ReferenceOrderedDatum.class))
 public class SelectVariants extends RodWalker<Integer, Integer> {
-    @Argument(fullName="sample", shortName="sn", doc="Sample(s) to include.  Can be a single sample, specified multiple times for many samples, or a regular expression to select many samples.", required=false)
+    @Argument(fullName="sample", shortName="sn", doc="Sample(s) to include.  Can be a single sample, specified multiple times for many samples, a file containing sample names, a regular expression to select many samples, or any combination thereof.", required=false)
     public Set<String> SAMPLE_EXPRESSIONS;
 
     @Argument(shortName="select", doc="One or more criteria to use when selecting the data.  Evaluated *after* the specified samples are extracted and the INFO-field annotations are updated.", required=false)
@@ -88,16 +92,38 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
         Set<String> vcfSamples = SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
 
         if (SAMPLE_EXPRESSIONS != null) {
-            // Let's first assume that the values in SAMPLE_EXPRESSIONS are literal sample names and not regular
+            // 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.
+            Set<String> samplesFromFiles = new HashSet<String>();
+            for (String SAMPLE_EXPRESSION : SAMPLE_EXPRESSIONS) {
+                File sampleFile = new File(SAMPLE_EXPRESSION);
+
+                try {
+                    XReadLines reader = new XReadLines(sampleFile);
+
+                    List<String> lines = reader.readLines();
+                    for (String line : lines) {
+                        samplesFromFiles.add(line);
+                    }
+                } catch (FileNotFoundException e) {
+                    // ignore exception
+                }
+            }
+
+            SAMPLE_EXPRESSIONS.addAll(samplesFromFiles);
+            
+            // Let's now assume that the values in SAMPLE_EXPRESSIONS are literal sample names and not regular
             // expressions.  Extract those samples specifically so we don't make the mistake of selecting more
             // than what the user really wants.
             for (String SAMPLE_EXPRESSION : SAMPLE_EXPRESSIONS) {
+                if (!(new File(SAMPLE_EXPRESSION).exists())) {
                     if (vcfSamples.contains(SAMPLE_EXPRESSION)) {
                         samples.add(SAMPLE_EXPRESSION);
                     } else {
                         possibleSampleRegexs.add(SAMPLE_EXPRESSION);
                     }
                 }
+            }
 
             // Now, check the expressions that weren't used in the previous step, and use them as if they're regular expressions
             for (String sampleRegex : possibleSampleRegexs) {

java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java

@@ -13,9 +13,10 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
     @Test
     public void testComplexSelection() {
         String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";
+        String samplesFile = validationDataLocation + "SelectVariants.samples.txt";
 
         WalkerTestSpec spec = new WalkerTestSpec(
-            baseTestString(" -sn A -sn '[CDEH]' -env -ef -select 'AF < 0.2' -B variant,VCF," + testfile),
+            baseTestString(" -sn A -sn '[CDH]' -sn " + samplesFile + " -env -ef -select 'AF < 0.2' -B variant,VCF," + testfile),
             1,
             Arrays.asList("3a15628b5980031c629c0c33e7e60b40")
         );