Fix FastqToSam regression. (#1811)

broadinstitute · Jun 1, 2022 · fc91208 · fc91208
1 parent 923403d
commit fc91208
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Showing 6 changed files with 4 additions and 20,008 deletions.
diff --git a/src/main/java/picard/sam/FastqToSam.java b/src/main/java/picard/sam/FastqToSam.java
@@ -435,11 +435,7 @@ protected int doPaired(final FastqReader freader1, final FastqReader freader2, f
     }
 
     private FastqReader fileToFastqReader(final Path path) throws PicardException {
-        try {
-            return new FastqReader(null, Files.newBufferedReader(path), ALLOW_AND_IGNORE_EMPTY_LINES);
-        } catch (IOException e){
-            throw new PicardException("cannot create a reader for " + path, e);
-        }
+        return new FastqReader(null, IOUtil.openFileForBufferedReading(path), ALLOW_AND_IGNORE_EMPTY_LINES);
     }
 
     private SAMRecord createSamRecord(final SAMFileHeader header, final String baseName, final FastqRecord frec, final boolean paired) {

diff --git a/src/test/java/picard/sam/CramCompatibilityTest.java b/src/test/java/picard/sam/CramCompatibilityTest.java
@@ -24,7 +24,7 @@ public class CramCompatibilityTest {
     public static final String CRAM_FILE_QUERY_SORTED = "testdata/picard/sam/test_cram_file_query_sorted.cram";
 
     public static final String REFERENCE_FILE = "testdata/picard/sam/test_cram_file.ref.fa";
-    public static final String FASTQ_FILE = "testdata/picard/sam/fastq2bam/fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq";
+    public static final String FASTQ_FILE = "testdata/picard/sam/fastq2bam/fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq.gz";
 
     public static final String CRAM_UNMAPPED = "testdata/picard/sam/SamFormatConverterTest/unmapped.cram";
     public static final String CRAM_UNMAPPED_WITH_OQ_TAG = "testdata/picard/sam/unmapped_with_oq_tag.cram";

diff --git a/src/test/java/picard/sam/FastqToSamTest.java b/src/test/java/picard/sam/FastqToSamTest.java
@@ -56,7 +56,7 @@ public String getCommandLineProgramName() {
     @DataProvider(name = "okVersionFiles")
     public Object[][] okVersionFiles() {
         return new Object[][] {
-            {"fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq",      FastqQualityFormat.Standard },
+            {"fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq.gz",      FastqQualityFormat.Standard },
             {"fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq",     FastqQualityFormat.Standard },
             {"fastq-sanger/sanger_full_range_as_sanger-63.fastq", FastqQualityFormat.Standard }, // all sanger chars