Java tutorial
/* The MIT License (MIT) Copyright (c) 2014 Pierre Lindenbaum 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. History: * 2014 creation */ package com.github.lindenb.jvarkit.tools.bam2wig; import java.io.PrintWriter; import java.util.Arrays; import java.util.Collection; import htsjdk.samtools.CigarOperator; import htsjdk.samtools.SamReader; import htsjdk.samtools.Cigar; import htsjdk.samtools.CigarElement; import htsjdk.samtools.SAMRecord; import htsjdk.samtools.SAMRecordIterator; import htsjdk.samtools.SAMSequenceDictionary; import htsjdk.samtools.SAMSequenceRecord; import htsjdk.samtools.util.CloserUtil; import com.github.lindenb.jvarkit.util.picard.SAMSequenceDictionaryProgress; public class Bam2Wig extends AbstractBam2Wig { private static final org.apache.commons.logging.Log LOG = org.apache.commons.logging.LogFactory .getLog(Bam2Wig.class); public Bam2Wig() { } private PrintWriter pw = null; private void run(final SamReader sfr) { SAMSequenceRecord prev_ssr = null; SAMSequenceDictionary dict = sfr.getFileHeader().getSequenceDictionary(); SAMRecordIterator iter = sfr.iterator(); int array[] = null; SAMSequenceDictionaryProgress progess = new SAMSequenceDictionaryProgress(dict); if (custom_track) { pw.println("track type=wiggle_0 name=\"__REPLACE_WIG_NAME__\" description=\"__REPLACE_WIG_DESC__\""); } for (;;) { SAMRecord rec = null; if (iter.hasNext()) { rec = iter.next(); progess.watch(rec); if (rec.getReadUnmappedFlag()) continue; if (rec.getMappingQuality() == 0) continue; if (rec.getMappingQuality() < min_qual) continue; } if (rec == null || (prev_ssr != null && prev_ssr.getSequenceIndex() != rec.getReferenceIndex())) { if (prev_ssr != null) { int start0 = 0; while (start0 < array.length && array[start0] == 0) { ++start0; } int end0 = prev_ssr.getSequenceLength(); while (end0 > 0 && array[end0 - 1] == 0) { --end0; } int last_non_zero_pos0 = start0; int num_zero_regions_skipped = 0; boolean need_print_header = true; while (start0 < end0) { /* * http://genome.ucsc.edu/goldenPath/help/wiggle.html Wiggle track data values can be integer or real, positive or negative values. Chromosome positions are specified as 1-relative. For a chromosome of length N, the first position is 1 and the last position is N. Only positions specified have data. Positions not specified do not have data and will not be graphed. */ int n = 0; double sum = 0; for (int j = 0; j < WINDOW_SIZE && start0 + j < array.length; ++j) { sum += array[start0 + j]; n++; } if (sum / n < min_depth) { sum = 0; } if (sum == 0) { start0 += WINDOW_SHIFT; num_zero_regions_skipped++; continue; } else { if ((start0 - last_non_zero_pos0) <= min_gap) { for (int r = 0; r < num_zero_regions_skipped; ++r) { pw.println(0); } } else { need_print_header = (num_zero_regions_skipped > 0); } last_non_zero_pos0 = start0; num_zero_regions_skipped = 0; } if (need_print_header) { need_print_header = false; pw.println("fixedStep chrom=" + prev_ssr.getSequenceName() + " start=" + (start0 + 1) + " step=" + WINDOW_SHIFT + " span=" + WINDOW_SIZE); } if (cast_to_integer) { pw.println((int) (sum / n)); } else { pw.println((float) (sum / n)); } if (pw.checkError()) break; start0 += WINDOW_SHIFT; } array = null; System.gc(); prev_ssr = null; } if (rec == null) break; if (pw.checkError()) break; } if (prev_ssr == null) { prev_ssr = dict.getSequence(rec.getReferenceIndex()); LOG.info("Allocating int[" + prev_ssr.getSequenceLength() + "]"); array = new int[prev_ssr.getSequenceLength()]; LOG.info("Allocating : Done."); Arrays.fill(array, 0); } final Cigar cigar = rec.getCigar(); if (cigar == null) continue; int refpos1 = rec.getAlignmentStart(); for (CigarElement ce : cigar.getCigarElements()) { final CigarOperator op = ce.getOperator(); if (op.consumesReferenceBases()) { if (op.consumesReadBases()) { for (int i = 0; i < ce.getLength() && refpos1 <= array.length; ++i) { if (refpos1 >= 1 && refpos1 <= array.length) { array[refpos1 - 1]++; } refpos1++; } } else { refpos1 += ce.getLength(); } } } } progess.finish(); iter.close(); pw.flush(); } @Override protected Collection<Throwable> call(String inputName) throws Exception { SamReader in = null; this.pw = openFileOrStdoutAsPrintWriter(); try { in = openSamReader(inputName); run(in); pw.flush(); return RETURN_OK; } catch (Exception err) { LOG.error(err); return wrapException(err); } finally { CloserUtil.close(in); CloserUtil.close(pw); pw = null; in = null; } } /** * @param args */ public static void main(String[] args) { new Bam2Wig().instanceMainWithExit(args); } }