added automated VCF indexing to VCF BED intersection code

src/vcfutils/VCFBedIntersect.java

@@ -42,12 +42,13 @@ public static void intersectBedAndVCF(Path vcfPath, Path bedPath, Path outputFol
 		VCFFileReader reader = null;
 		//VCFUtils.createTemporaryIndexedVcfFromInput(vcfPath.toFile(), "temp");
 		File tempFile = vcfPath.toFile();
+		File file2 = VCFUtils.createTemporaryIndexedVcfFromInput(tempFile, "temp_");
 
 		Path outputVcf = outputFolder.resolve("intersected.vcf");
 
 
 		//tempFile = VCFUtils.createTemporaryIndexedVcfFromInput(vcfPath.toFile(), "temp");
-		reader = new VCFFileReader(tempFile); 
+		reader = new VCFFileReader(file2); 
 
 
 
@@ -87,8 +88,9 @@ public static void intersectBedAndVCF(Path vcfPath, Path bedPath, Path outputFol
 			vcfWriter.close();
 		}
 
-
-
+		file2.delete();
+		File file4 = new File(file2.toString()+".idx");
+		file4.delete();
 
 
 

target/maven-status/maven-compiler-plugin/compile/default-compile/createdFiles.lst

@@ -0,0 +1,82 @@
+com\psl\automation\panels\VcfBedIntersectionPanel$4.class
+com\psl\swingexample\JIFrameDemo$1.class
+com\psl\swingexample\OpenMenu.class
+com\psl\automation\panels\QCComparePanel$1.class
+com\psl\swingexample\DisplayGraphics.class
+com\psl\swingexample\JIFrameDemo.class
+com\psl\swingexample\Notepad.class
+vcfutils\ComparisonResult.class
+com\psl\automation\main\FileChooserDemo.class
+com\psl\automation\panels\CompareVcfPanel$6.class
+com\psl\automation\main\MainGui$2.class
+com\psl\automation\main\Interval.class
+com\psl\automation\panels\BarcodeMetricsPanel$1.class
+com\psl\automation\panels\CompareVcfPanel$2.class
+com\psl\automation\panels\BedUtilitiesPanel$3.class
+com\psl\automation\panels\QCComparePanel$5.class
+com\psl\automation\panels\TsTvMetricsPanel$2.class
+vcfutils\VCFrecord.class
+com\psl\automation\panels\CompareVcfPanel$5.class
+com\psl\automation\panels\CompareVcfPanel.class
+com\psl\automation\panels\VcfBedIntersectionPanel.class
+hsutils\BAMParser.class
+liftoverutils\BedInterval.class
+com\psl\automation\fileCompare\VCFrecord.class
+com\psl\automation\panels\TsTvMetricsPanel.class
+com\psl\swingexample\JIFrameDemo$2.class
+com\psl\automation\panels\TsTvMetricsPanel$1.class
+com\psl\automation\panels\QCComparePanel$4.class
+vcfutils\VCFUtils.class
+hsutils\BamSorter.class
+gatkUtils\StreamGobbler.class
+liftoverutils\IntervalUtils.class
+vcfutils\VariantExceptions.class
+vcfutils\TsTvStatistics$1.class
+com\psl\automation\panels\VcfBedIntersectionPanel$3.class
+com\psl\automation\panels\BedUtilitiesPanel$2.class
+com\psl\automation\panels\BarcodeMetricsPanel.class
+com\psl\automation\panels\BedUtilitiesPanel.class
+vcfutils\CompareUtils.class
+liftoverutils\LiftOverDriver.class
+vcfutils\TsTvStatistics.class
+com\psl\swingexample\MyProgress.class
+gatkUtils\GatkThread.class
+com\psl\automation\main\MainGui.class
+qcutils\QCMetricsCompare.class
+com\psl\automation\panels\LiftOverUtilPanel.class
+liftoverutils\Chain.class
+com\psl\automation\main\MainGui$TabSelected.class
+com\psl\automation\panels\QCComparePanel$3.class
+gatkUtils\GatkUtils.class
+com\psl\automation\panels\CompareVcfPanel$1.class
+com\psl\swingexample\DigitalWatch.class
+qcutils\QCCompareResults.class
+com\psl\automation\main\MainGui$1.class
+com\psl\automation\panels\CompareVcfPanel$4.class
+com\psl\automation\panels\QCComparePanel.class
+com\psl\automation\main\BigTextField$1.class
+hsutils\TestAl.class
+com\psl\automation\panels\QCComparePanel$2.class
+com\psl\automation\panels\VcfBedIntersectionPanel$2.class
+liftoverutils\Interval.class
+com\psl\automation\main\FileChooserDemo$1.class
+com\psl\automation\panels\BedUtilitiesPanel$1.class
+com\psl\automation\annotation\Driver.class
+com\psl\automation\annotation\VariationReporter.class
+vcfutils\VCFBedIntersect.class
+com\psl\swingexample\MainScreen.class
+com\psl\automation\main\BigTextField.class
+bedUtils\BedUtils.class
+vcfutils\VariantTypes.class
+com\psl\automation\panels\BedUtilitiesPanel$4.class
+vcfutils\TsTvStatistics$2.class
+bedUtils\Chromosome.class
+com\psl\swingexample\FirstSwingExample.class
+com\psl\automation\panels\BarcodeMetricsPanel$2.class
+com\psl\automation\panels\CompareVcfPanel$3.class
+com\psl\automation\panels\VcfBedIntersectionPanel$1.class
+liftoverutils\ChainException.class
+com\psl\automation\panels\TsTvMetricsPanel$3.class
+liftoverutils\IntervalTree.class
+vcfutils\TestVCFreader.class
+liftoverutils\IntervalNode.class