Added tests of LINE_LENGTH and TRUNCATE_SEQ...

broadinstitute · Sep 4, 2015 · 7a26db2 · 7a26db2
1 parent 014624e
commit 7a26db2
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Showing 4 changed files with 23 additions and 4 deletions.
diff --git a/.../java/org/broadinstitute/hellbender/tools/picard/fastq/NormalizeFastaIntegrationTest.java b/.../java/org/broadinstitute/hellbender/tools/picard/fastq/NormalizeFastaIntegrationTest.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.hellbender.tools.picard.fastq;
 
 import org.broadinstitute.hellbender.CommandLineProgramTest;
-
 import org.broadinstitute.hellbender.tools.IntegrationTestSpec;
 import org.broadinstitute.hellbender.utils.test.BaseTest;
 import org.testng.annotations.Test;
@@ -16,20 +15,24 @@
     public final class NormalizeFastaIntegrationTest extends CommandLineProgramTest {
 
         private static final File TEST_DATA_PATH = new File(getTestDataDir(), "picard/fasta/" );
+
     public String getTestedClassName() {
+
         return NormalizeFasta.class.getSimpleName();
     }
 
         @Test
         public void testNormalize () throws IOException {
 
-            final File input = new File(TEST_DATA_PATH, "truncatedFASTA.fasta");
-            final File expectedFile = new File(TEST_DATA_PATH, "truncatedFASTA2.fasta");
+            final File input = new File(TEST_DATA_PATH, "truncatedFASTA_WS.fasta");
+            final File expectedFile = new File(TEST_DATA_PATH, "truncatedFASTA_WS_2.fasta");
             final File outfile = BaseTest.createTempFile("normalized", ".fasta");
 
             final String[] args = {
                     "--INPUT", input.getAbsolutePath(),
                     "--OUTPUT", outfile.getAbsolutePath(),
+                    "--TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE", "TRUE",
+
 
             };
 

diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/picard/fasta/truncatedFASTA_2.fasta b/src/test/resources/org/broadinstitute/hellbender/tools/picard/fasta/truncatedFASTA_2.fasta
@@ -0,0 +1,8 @@
+>chr1
+taaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaac
+cctaacccaaccctaaccctaaccctaaccctaaccctaaccctaacccctaaccctaaccctaaccctaaccctaacctaaccctaaccctaaccctaa
+ccctaaccctaaccctaaccctaaccctaacccctaaccctaaccctaaaccctaaaccctaaccctaaccctaaccctaaccctaaccccaaccccaac
+CCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCA
+CAGGGTCTTGATGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCT
+GTGGAGAGGAGCCATGCCTAGAGTGGGATGGGCCATTGTTCATCTTCTGGCCCCTGTTGTCTGCATGTAACTTAATACCACAACCAGGCATAGGGGAAAG
+ATTGGAGGAAAGATGAGTGAGAGCATCAACTTCTCTCACAACCTAGGCCAGTAAGTAGTG
diff --git a/...test/resources/org/broadinstitute/hellbender/tools/picard/fasta/truncatedFASTA_WS_2.fasta b/...test/resources/org/broadinstitute/hellbender/tools/picard/fasta/truncatedFASTA_WS_2.fasta
@@ -0,0 +1,8 @@
+>chromosome
+taaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaac
+cctaacccaaccctaaccctaaccctaaccctaaccctaaccctaacccctaaccctaaccctaaccctaaccctaacctaaccctaaccctaaccctaa
+ccctaaccctaaccctaaccctaaccctaacccctaaccctaaccctaaaccctaaaccctaaccctaaccctaaccctaaccctaaccccaaccccaac
+CCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCA
+CAGGGTCTTGATGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCT
+GTGGAGAGGAGCCATGCCTAGAGTGGGATGGGCCATTGTTCATCTTCTGGCCCCTGTTGTCTGCATGTAACTTAATACCACAACCAGGCATAGGGGAAAG
+ATTGGAGGAAAGATGAGTGAGAGCATCAACTTCTCTCACAACCTAGGCCAGTAAGTAGTG
diff --git a/.../tools/picard/fasta/truncatedFASTA2.fasta → ...ools/picard/fasta/truncatedFasta_WS.fasta b/.../tools/picard/fasta/truncatedFASTA2.fasta → ...ools/picard/fasta/truncatedFasta_WS.fasta
@@ -1,4 +1,4 @@
->chr1
+>chromosome 1
 taaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccc
 taaccctaaccctaaccctaaccctaaccctaaccctaaccctaacccaaccctaaccct
 aaccctaaccctaaccctaaccctaacccctaaccctaaccctaaccctaaccctaacct