// Copyright (c) 2010 Aalto University // // Permission is hereby granted, free of charge, to any person obtaining a copy // of this software and associated documentation files (the "Software"), to // deal in the Software without restriction, including without limitation the // rights to use, copy, modify, merge, publish, distribute, sublicense, and/or // sell copies of the Software, and to permit persons to whom the Software is // furnished to do so, subject to the following conditions: // // The above copyright notice and this permission notice shall be included in // all copies or substantial portions of the Software. // // THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR // IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, // FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE // AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER // LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING // FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS // IN THE SOFTWARE. // File created: 2010-08-20 13:54:10 package org.seqdoop.hadoop_bam.util; import java.io.File; import java.io.FileOutputStream; import java.io.IOException; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SamReaderFactory; import htsjdk.samtools.ValidationStringency; import org.seqdoop.hadoop_bam.SAMFormat; public final class GetSortedBAMHeader { public static void main(String[] args) throws IOException { if (args.length < 2) { System.err.println( "Usage: GetSortedBAMHeader input output\n\n"+ "Reads the BAM header from input (a standard BGZF-compressed BAM "+ "file), and\nwrites it (BGZF-compressed, no terminator block) to "+ "output. Sets the sort order\nindicated in the SAM header to "+ "'coordinate'."); System.exit(1); } final SAMFileHeader h = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT) .setUseAsyncIo(false) .open(new File(args[0])).getFileHeader(); h.setSortOrder(SAMFileHeader.SortOrder.coordinate); try (FileOutputStream stream = new FileOutputStream(args[1])) { new SAMOutputPreparer().prepareForRecords(stream, SAMFormat.BAM, h); } } }