From 8bd39611e4207feb4428b4830ebe1a52160bfe6d Mon Sep 17 00:00:00 2001 From: DavidAustinNix Date: Tue, 31 Mar 2020 12:34:14 -0600 Subject: [PATCH] Fixed an issue where fetching the header from some bams was causing a null pointer error. --- Source/edu/utah/seq/parsers/MergePairedAlignments.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Source/edu/utah/seq/parsers/MergePairedAlignments.java b/Source/edu/utah/seq/parsers/MergePairedAlignments.java index c89c5202..9ba01e46 100644 --- a/Source/edu/utah/seq/parsers/MergePairedAlignments.java +++ b/Source/edu/utah/seq/parsers/MergePairedAlignments.java @@ -397,7 +397,7 @@ private void saveHeader() throws FileNotFoundException, IOException { SamReaderFactory readerFactory = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT); SamReader bamReader = readerFactory.open(bamFile); SAMFileHeader h = bamReader.getFileHeader(); - String[] shLines = Misc.RETURN.split(h.getTextHeader()); //this gets the original header, setting SamSort.unsorted doesn't change it. Ugg. + String[] shLines = Misc.RETURN.split(h.getSAMString()); //this gets the original header, setting SamSort.unsorted doesn't change it. Ugg. bamReader.close(); for (int i=0; i< shLines.length; i++){ if (shLines[i].contains("SO:coordinate")){ @@ -418,7 +418,7 @@ private void saveHeader() throws FileNotFoundException, IOException { public static void printDocs(){ System.out.println("\n" + "**************************************************************************************\n" + - "** Merge Paired Alignments: Mar 2020 **\n" + + "** Merge Paired Alignments: March 2020 **\n" + "**************************************************************************************\n" + "Merges proper paired alignments that pass a variety of checks and thresholds. Only\n" + "unambiguous pairs will be merged. Increases base calling accuracy in overlap and helps\n" +