From da5e567b73c2139e3cfb5847a4b33ad7588bab94 Mon Sep 17 00:00:00 2001
From: Phillip Dexheimer <phildex@broadinstitute.org>
Date: Tue, 17 Jun 2014 23:38:03 -0400
Subject: [PATCH] Added functionality to CatVariants to process .list files
 with -V  - Pivotal 70305712

---
 .../gatk/tools/CatVariants.java               | 25 +++++++++++++++++++
 .../tools/CatVariantsIntegrationTest.java     |  5 ++++
 2 files changed, 30 insertions(+)

diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/CatVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/CatVariants.java
index 631e8e015..43403ab79 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/CatVariants.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/CatVariants.java
@@ -38,6 +38,7 @@ import org.broadinstitute.gatk.utils.commandline.Output;
 import org.broadinstitute.gatk.utils.commandline.CommandLineProgram;
 import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.text.XReadLines;
 import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType;
 import org.broadinstitute.gatk.utils.variant.GATKVCFUtils;
 import htsjdk.variant.bcf2.BCF2Codec;
@@ -196,6 +197,28 @@ public class CatVariants extends CommandLineProgram {
         return reader;
     }
 
+    /**
+     * Replaces any .list files in rawFileList with the files named in said .list file
+     * @param rawFileList the original file list, possibly including .list files
+     * @return a new List, with .list files replaced
+     */
+    private List<File> parseVariantList(final List<File> rawFileList) {
+        final List<File> result = new ArrayList<>(rawFileList.size());
+        for (final File rawFile : rawFileList) {
+            if (rawFile.getName().endsWith(".list")) {
+                try {
+                    for (final String line : new XReadLines(rawFile, true))
+                        result.add(new File(line));
+                } catch (IOException e) {
+                    throw new UserException.CouldNotReadInputFile(rawFile, e);
+                }
+            } else {
+                result.add(rawFile);
+            }
+        }
+        return result;
+    }
+
     @Override
     protected int execute() throws Exception {
         BasicConfigurator.configure();
@@ -208,6 +231,8 @@ public class CatVariants extends CommandLineProgram {
             throw new UserException("Couldn't load provided reference sequence file " + refFile, e);
         }
 
+        variant = parseVariantList(variant);
+
         Comparator<Pair<Integer,File>> positionComparator = new PositionComparator();
 
         Queue<Pair<Integer,File>> priorityQueue;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/CatVariantsIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/CatVariantsIntegrationTest.java
index 849267317..07ac8ab5d 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/CatVariantsIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/CatVariantsIntegrationTest.java
@@ -78,6 +78,11 @@ public class CatVariantsIntegrationTest {
         for (String extension : AbstractFeatureReader.BLOCK_COMPRESSED_EXTENSIONS)
             new CatVariantsTestProvider("CatVariantsTest1.vcf" + extension, "CatVariantsTest2.vcf" + extension, BaseTest.createTempFile("CatVariantsTest", ".vcf" + extension), "33f728ac5c70ce2994f3619a27f47088");
 
+        //Test list parsing functionality
+        new CatVariantsTestProvider("CatVariantsTest1.list", "CatVariantsTest2.vcf", BaseTest.createTempFile("CatVariantsTest", ".vcf"), "d0d81eb7fd3905256c4ac7c0fc480094");
+        new CatVariantsTestProvider("CatVariantsTest1.vcf", "CatVariantsTest2.list", BaseTest.createTempFile("CatVariantsTest", ".vcf"), "d0d81eb7fd3905256c4ac7c0fc480094");
+        new CatVariantsTestProvider("CatVariantsTest1.list", "CatVariantsTest2.list", BaseTest.createTempFile("CatVariantsTest", ".vcf"), "d0d81eb7fd3905256c4ac7c0fc480094");
+
         return CatVariantsTestProvider.getTests(CatVariantsTestProvider.class);
     }