/*
* Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard. All Rights Reserved.
*
* This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
* Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
*
* THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR
* WARRANTES OF ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING,
* WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
* PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER
* OR NOT DISCOVERABLE. IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR RESPECTIVE
* TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES
* OF ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES,
* ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER
* THE BROAD OR MIT SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT
* SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
*/
/*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.broad.igv.sam.reader;
import org.apache.log4j.Logger;
import org.broad.igv.Globals;
import org.broad.igv.sam.DotAlignedAlignment;
import org.broad.igv.util.ParsingUtils;
import htsjdk.tribble.readers.AsciiLineReader;
import java.io.IOException;
/**
* @author jrobinso
*/
public class DotAlignedParser implements AlignmentParser {
private static Logger log = Logger.getLogger(DotAlignedParser.class);
public static int CHROMOSOME_COLUMN = 0;
private static int START_COLUMN = 1;
private static int END_COLUMN = 2;
private static int STRAND_COLUMN = 3;
private static int NAME_COLUMN = -1;
boolean bedFormat = false;
public DotAlignedParser() {
bedFormat = false;
}
public DotAlignedParser(boolean bedFormat) {
this.bedFormat = bedFormat;
if (bedFormat) {
STRAND_COLUMN = 5;
NAME_COLUMN = 3;
}
}
public DotAlignedAlignment readNextRecord(AsciiLineReader reader) {
String nextLine;
try {
while ((nextLine = reader.readLine()) != null) {
DotAlignedAlignment alignment = createAlignment(nextLine);
if (alignment != null) {
return alignment;
}
}
} catch (IOException e) {
log.error("Error reading line", e);
}
return null;
}
private DotAlignedAlignment createAlignment(String nextLine) {
try {
String[] fields = Globals.tabPattern.split(nextLine, -1);
int nTokens = fields.length;
if (nTokens <= END_COLUMN) {
System.out.println("Skipping line: " + nextLine);
return null;
}
String chr = fields[CHROMOSOME_COLUMN];
int start = Integer.parseInt(fields[START_COLUMN]);
int end = Integer.parseInt(fields[END_COLUMN]);
if (bedFormat) {
boolean isNegative = false;
String name = "";
if (nTokens > STRAND_COLUMN) {
isNegative = fields[STRAND_COLUMN].equals("-");
}
if (nTokens > NAME_COLUMN) {
name = fields[NAME_COLUMN];
}
return new DotAlignedAlignment(chr, start, end, isNegative, name);
} else {
boolean isNegative = fields[STRAND_COLUMN].equals("-");
return new DotAlignedAlignment(chr, start, end, isNegative);
}
} catch (NumberFormatException e) {
System.out.println("Skipping line: " + nextLine);
return null;
}
}
}