From 3253fc216b8eb77859911ba0fb73b27509aa89c1 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 16 Aug 2012 15:53:06 -0400 Subject: [PATCH] FindBugs 'Maintainability' fixes --- .../net/sf/picard/reference/FastaSequenceIndexBuilder.java | 1 + .../gatk/walkers/diagnostics/targets/SampleStatistics.java | 2 +- .../sting/gatk/walkers/diffengine/BAMDiffableReader.java | 4 +++- .../gatk/walkers/diffengine/GATKReportDiffableReader.java | 6 ++++-- .../gatk/walkers/indels/ConstrainedMateFixingManager.java | 2 +- .../gatk/walkers/variantrecalibration/TrancheManager.java | 1 + .../gatk/walkers/variantutils/VariantsToBinaryPed.java | 1 + .../org/broadinstitute/sting/utils/help/ForumAPIUtils.java | 1 + 8 files changed, 13 insertions(+), 5 deletions(-) diff --git a/public/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java b/public/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java index 6c8fe1834..10326ef2e 100644 --- a/public/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java +++ b/public/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java @@ -208,6 +208,7 @@ public class FastaSequenceIndexBuilder { break; } } + in.close(); return sequenceIndex; } catch (IOException e) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatistics.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatistics.java index 0fc2d8929..9f6258eee 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatistics.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatistics.java @@ -264,7 +264,7 @@ class SampleStatistics { return false; // different contigs - if (read.getMateReferenceIndex() != read.getReferenceIndex()) + if (!read.getMateReferenceIndex().equals(read.getReferenceIndex())) return false; // unmapped diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java index 2d372ca9f..0d4db5560 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java @@ -104,7 +104,9 @@ public class BAMDiffableReader implements DiffableReader { InputStream fstream = new BufferedInputStream(new FileInputStream(file)); if ( !BlockCompressedInputStream.isValidFile(fstream) ) return false; - new BlockCompressedInputStream(fstream).read(buffer, 0, BAM_MAGIC.length); + final BlockCompressedInputStream BCIS = new BlockCompressedInputStream(fstream); + BCIS.read(buffer, 0, BAM_MAGIC.length); + BCIS.close(); return Arrays.equals(buffer, BAM_MAGIC); } catch ( IOException e ) { return false; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java index 480a1fc29..5e4ea5f81 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java @@ -90,8 +90,10 @@ public class GATKReportDiffableReader implements DiffableReader { public boolean canRead(File file) { try { final String HEADER = GATKReport.GATKREPORT_HEADER_PREFIX; - char[] buff = new char[HEADER.length()]; - new FileReader(file).read(buff, 0, HEADER.length()); + final char[] buff = new char[HEADER.length()]; + final FileReader FR = new FileReader(file); + FR.read(buff, 0, HEADER.length()); + FR.close(); String firstLine = new String(buff); return firstLine.startsWith(HEADER); } catch (IOException e) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java index 4feba35af..68365adf7 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java @@ -305,7 +305,7 @@ public class ConstrainedMateFixingManager { } public static boolean iSizeTooBigToMove(SAMRecord read, int maxInsertSizeForMovingReadPairs) { - return ( read.getReadPairedFlag() && ! read.getMateUnmappedFlag() && read.getReferenceName() != read.getMateReferenceName() ) // maps to different chromosomes + return ( read.getReadPairedFlag() && ! read.getMateUnmappedFlag() && !read.getReferenceName().equals(read.getMateReferenceName()) ) // maps to different chromosomes || Math.abs(read.getInferredInsertSize()) > maxInsertSizeForMovingReadPairs; // we won't try to move such a read } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java index d45739528..af0778399 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java @@ -177,6 +177,7 @@ public class TrancheManager { double runningValue = metric.getRunningMetric(i); out.printf("%.4f %d %.4f%n", d.lod, score, runningValue); } + out.close(); } catch (FileNotFoundException e) { throw new UserException.CouldNotCreateOutputFile(f, e); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java index 14c811b03..3fba8fa77 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java @@ -270,6 +270,7 @@ public class VariantsToBinaryPed extends RodWalker { inStream.read(readGenotypes); outBed.write(readGenotypes); } + inStream.close(); } catch (IOException e) { throw new ReviewedStingException("Error reading form temp file for input.",e); } diff --git a/public/java/src/org/broadinstitute/sting/utils/help/ForumAPIUtils.java b/public/java/src/org/broadinstitute/sting/utils/help/ForumAPIUtils.java index 388e7ce45..1dfc4ecc0 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/ForumAPIUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/ForumAPIUtils.java @@ -135,6 +135,7 @@ public class ForumAPIUtils { System.out.println(line); } + br.close(); httpClient.getConnectionManager().shutdown(); return output;