/*
* 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.
*/
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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;
}
}
}