/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* 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.
*/
package org.broad.igv.sam.reader;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMReadGroupRecord;
import htsjdk.samtools.SamReaderFactory;
import htsjdk.samtools.ValidationStringency;
import org.apache.log4j.Logger;
import org.broad.igv.exceptions.DataLoadException;
import org.broad.igv.ga4gh.Ga4ghAlignmentReader;
import org.broad.igv.ga4gh.Ga4ghProvider;
import org.broad.igv.goby.GobyAlignmentQueryReader;
import org.broad.igv.util.FileUtils;
import org.broad.igv.util.ParsingUtils;
import org.broad.igv.util.ResourceLocator;
import java.io.BufferedReader;
import java.io.IOException;
import java.util.*;
/**
* @author jrobinso
*/
public class AlignmentReaderFactory {
private static Logger log = Logger.getLogger(AlignmentReaderFactory.class);
static {
SamReaderFactory.setDefaultValidationStringency(ValidationStringency.SILENT);
}
public static AlignmentReader getReader(String path, boolean requireIndex) throws IOException {
return getReader(new ResourceLocator(path), requireIndex);
}
public static AlignmentReader getReader(ResourceLocator locator) throws IOException {
return getReader(locator, true);
}
public static AlignmentReader getReader(ResourceLocator locator, boolean requireIndex) throws IOException {
log.debug("Getting alignment reader for " + locator);
String pathLowerCase = locator.getPath().toLowerCase();
AlignmentReader reader = null;
String samFile = locator.getPath();
String typeString = locator.getTypeString();
if ("alist".equals(locator.getType())) {
reader = getMergedReader(locator.getPath(), true);
} else if (pathLowerCase.startsWith("http") && pathLowerCase.contains("/query.cgi?")) {
reader = new CGIAlignmentReader(samFile);
} else if (typeString.endsWith(".sam")) {
reader = new SAMReader(samFile, requireIndex);
} else if (typeString.endsWith(".aligned")
|| typeString.endsWith(".aligned.txt")
|| typeString.endsWith("bedz")
|| typeString.endsWith("bed")
|| typeString.endsWith("psl")
|| typeString.endsWith("pslx")) {
reader = new GeraldReader(samFile, requireIndex);
} else if (typeString.endsWith(".bam") || (typeString.endsWith(".cram"))) {
try {
reader = new BAMReader(locator, requireIndex); //, requireIndex);
} catch (Exception e) {
log.error(e.getMessage(), e);
throw new DataLoadException("Error loading BAM file: " + e.toString(), locator.getPath());
}
} else if (typeString.endsWith(".bam.list") || pathLowerCase.endsWith(".sam.list")) {
reader = getBamListReader(locator.getPath(), requireIndex);
} else if (GobyAlignmentQueryReader.supportsFileType(locator.getPath())) {
try {
reader = new GobyAlignmentQueryReader(locator.getPath());
} catch (IOException e) {
throw new RuntimeException("Cannot load Goby alignment " + locator.getPath(), e);
}
} else if (Ga4ghAlignmentReader.supportsFileType(locator.getType())) {
Ga4ghProvider provider = (Ga4ghProvider) locator.getAttribute("provider");
return new Ga4ghAlignmentReader(provider, locator.getPath());
} else {
throw new RuntimeException("Cannot find reader for aligment file: " + locator.getPath());
}
return reader;
}
static AlignmentReader getBamListReader(String listFile, boolean requireIndex) {
List<AlignmentReader> readers = new ArrayList();
BufferedReader reader = null;
try {
reader = ParsingUtils.openBufferedReader(listFile);
Map<String, String> replacements = new HashMap();
String nextLine = null;
while ((nextLine = reader.readLine()) != null) {
if (nextLine.startsWith("#replace")) {
String[] tokens = nextLine.split("\\s+");
if (tokens.length == 2) {
String[] kv = tokens[1].split("=");
if (kv.length == 2)
replacements.put(kv[0], kv[1]);
}
} else {
String f = nextLine.trim();
if (f.length() == 0) continue; // Empty line
for (Map.Entry<String, String> entry : replacements.entrySet()) {
f = f.replace(entry.getKey(), entry.getValue());
}
f = FileUtils.getAbsolutePath(f, listFile);
readers.add(AlignmentReaderFactory.getReader(f, requireIndex));
}
}
if (readers.size() == 1) {
return readers.get(0);
} else {
return new MergedAlignmentReader(readers);
}
} catch (IOException e) {
log.error("Error parsing " + listFile, e);
throw new RuntimeException("Error parsing: " + listFile + " (" + e.toString() + ")");
} finally {
if (reader != null) {
try {
reader.close();
} catch (IOException e) {
}
}
}
}
public static AlignmentReader getMergedReader(String alignmentFileList, boolean requireIndex) {
String aFile = null;
try {
String[] alignmentFiles = ParsingUtils.COMMA_PATTERN.split(alignmentFileList);
List<AlignmentReader> readers = new ArrayList(alignmentFiles.length);
for (String f : alignmentFiles) {
aFile = f;
readers.add(AlignmentReaderFactory.getReader(aFile, requireIndex));
}
if (readers.size() == 1) {
return readers.get(0);
} else {
return new MergedAlignmentReader(readers);
}
} catch (IOException e) {
log.error("Error instantiating reader for: " + aFile, e);
throw new RuntimeException("Error instantiating reader for : " + aFile + " (" + e.toString() + ")");
}
}
/**
* @param header
* @return Return the set of platforms, uppercase. Will be null iff header is null
*/
public static Set<String> getPlatforms(SAMFileHeader header) {
Set<String> platforms = null;
if (header != null) {
List<SAMReadGroupRecord> readGroups = header.getReadGroups();
if (readGroups != null) {
platforms = new HashSet<String>();
for (SAMReadGroupRecord rg : readGroups) {
String platform = rg.getPlatform();
if (platform != null) {
platforms.add(platform.toUpperCase());
}
}
}
}
// Hack for Moleculo
if(header.getProgramRecord("MAFtoSAM") != null) {
platforms.add("MOLECULO");
}
return platforms;
}
}