org.seqdoop.hadoop_bam.cli.plugins.View Maven / Gradle / Ivy
Go to download
Show more of this group Show more artifacts with this name
Show all versions of hadoop-bam Show documentation
Show all versions of hadoop-bam Show documentation
A Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework.
// Copyright (c) 2011 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: 2011-06-14 13:38:57
package org.seqdoop.hadoop_bam.cli.plugins;
import java.io.File;
import java.util.ArrayList;
import java.util.List;
import java.util.Locale;
import java.util.StringTokenizer;
import htsjdk.samtools.BamFileIoUtils;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.ValidationStringency;
import htsjdk.samtools.SAMFileWriterImpl;
import htsjdk.samtools.SAMFormatException;
import htsjdk.samtools.SAMRecordIterator;
import htsjdk.samtools.SAMSequenceRecord;
import htsjdk.samtools.SAMTextWriter;
import htsjdk.samtools.ValidationStringency;
import htsjdk.samtools.seekablestream.SeekableStream;
import org.apache.hadoop.fs.Path;
import org.seqdoop.hadoop_bam.SAMFormat;
import org.seqdoop.hadoop_bam.cli.CLIPlugin;
import org.seqdoop.hadoop_bam.cli.Utils;
import org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser;
import org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option.BooleanOption;
import org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option.StringOption;
import org.seqdoop.hadoop_bam.util.Pair;
import org.seqdoop.hadoop_bam.util.WrapSeekable;
public final class View extends CLIPlugin {
private static final List> optionDescs
= new ArrayList>();
private static final CmdLineParser.Option
headerOnlyOpt = new BooleanOption('H', "header-only"),
formatOpt = new StringOption ('F', "format=FMT"),
stringencyOpt = new StringOption("validation-stringency=S");
public View() {
super("view", "SAM and BAM viewing", "1.2", "PATH [regions...]",
optionDescs,
"Reads the BAM or SAM file in PATH and, by default, outputs it in "+
"SAM format. If any number of regions is given, only the alignments "+
"overlapping with those regions are output. Then an index is also "+
"required, expected at PATH.bai by default."+
"\n\n"+
"Regions can be given as only reference sequence names or indices "+
"like 'chr1', or with position ranges as well like 'chr1:100-200'. "+
"These coordinates are 1-based, with 0 representing the start or "+
"end of the sequence.");
}
static {
optionDescs.add(new Pair(
headerOnlyOpt, "print header only"));
optionDescs.add(new Pair(
formatOpt, "select the output format based on FMT: SAM or BAM"));
optionDescs.add(new Pair(
stringencyOpt, Utils.getStringencyOptHelp()));
}
// We suppress deprecation warnings for htsjdk.samtools.SAMFileReader since the
// alternative, SamReader, does not support the isBinary method.
@SuppressWarnings("deprecation")
@Override protected int run(CmdLineParser parser) {
final List args = parser.getRemainingArgs();
if (args.isEmpty()) {
System.err.println("view :: PATH not given.");
return 3;
}
Utils.toStringency(parser.getOptionValue(stringencyOpt, ValidationStringency.DEFAULT_STRINGENCY.toString()), "view");
final String path = args.get(0);
final List regions = args.subList(1, args.size());
final boolean headerOnly = parser.getBoolean(headerOnlyOpt);
final htsjdk.samtools.SAMFileReader reader;
try {
final Path p = new Path(path);
SeekableStream idx;
try {
idx = WrapSeekable.openPath(getConf(), p.suffix(".bai"));
} catch (Exception e) {
idx = null;
}
final SeekableStream sam = WrapSeekable.openPath(getConf(), p);
reader = idx == null ? new htsjdk.samtools.SAMFileReader(sam, false)
: new htsjdk.samtools.SAMFileReader(sam, idx, false);
} catch (Exception e) {
System.err.printf("view :: Could not open '%s': %s\n",
path, e.getMessage());
return 4;
}
reader.setValidationStringency(ValidationStringency.SILENT);
final SAMFileHeader header;
try {
header = reader.getFileHeader();
} catch (SAMFormatException e) {
System.err.printf("view :: Could not parse '%s': %s\n",
path, e.getMessage());
return 4;
}
final String fmt = (String)parser.getOptionValue(formatOpt);
final SAMFormat format =
fmt == null ? SAMFormat.SAM
: SAMFormat.valueOf(fmt.toUpperCase(Locale.ENGLISH));
final SAMFileWriterImpl writer;
switch (format) {
case BAM:
// BAM output inside view no longer supported since Picard made the class private
System.err.println("BAM output inside view no longer supported");
return 1;
case SAM:
writer = new SAMTextWriter(System.out);
break;
default: writer = null; assert false;
}
writer.setSortOrder(header.getSortOrder(), true);
writer.setHeader(header);
if (regions.isEmpty() || headerOnly) {
if (!headerOnly)
if (!writeIterator(writer, reader.iterator(), path))
return 4;
writer.close();
return 0;
}
if (!reader.isBinary()) {
System.err.println("view :: Cannot output regions from SAM file");
return 4;
}
if (!reader.hasIndex()) {
System.err.println(
"view :: Cannot output regions from BAM file lacking an index");
return 4;
}
reader.enableIndexCaching(true);
boolean errors = false;
for (final String region : regions) {
final StringTokenizer st = new StringTokenizer(region, ":-");
final String refStr = st.nextToken();
final int beg, end;
if (st.hasMoreTokens()) {
beg = parseCoordinate(st.nextToken());
end = st.hasMoreTokens() ? parseCoordinate(st.nextToken()) : -1;
if (beg < 0 || end < 0) {
errors = true;
continue;
}
if (end < beg) {
System.err.printf(
"view :: Invalid range, cannot end before start: '%d-%d'\n",
beg, end);
errors = true;
continue;
}
} else
beg = end = 0;
SAMSequenceRecord ref = header.getSequence(refStr);
if (ref == null) try {
ref = header.getSequence(Integer.parseInt(refStr));
} catch (NumberFormatException e) {}
if (ref == null) {
System.err.printf(
"view :: Not a valid sequence name or index: '%s'\n", refStr);
errors = true;
continue;
}
final SAMRecordIterator it =
reader.queryOverlapping(ref.getSequenceName(), beg, end);
if (!writeIterator(writer, it, path))
return 4;
}
writer.close();
return errors ? 5 : 0;
}
private boolean writeIterator(
SAMFileWriterImpl writer, SAMRecordIterator it, String path)
{
try {
while (it.hasNext())
writer.addAlignment(it.next());
return true;
} catch (SAMFormatException e) {
writer.close();
System.err.printf("view :: Could not parse '%s': %s\n",
path, e.getMessage());
return false;
}
}
private int parseCoordinate(String s) {
int c;
try {
c = Integer.parseInt(s);
} catch (NumberFormatException e) {
c = -1;
}
if (c < 0)
System.err.printf("view :: Not a valid coordinate: '%s'\n", s);
return c;
}
}
© 2015 - 2025 Weber Informatics LLC | Privacy Policy