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* Copyright (c) 2012 The Broad Institute
*
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* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
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*
* 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,
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package org.broadinstitute.gatk.engine.datasources.reads;
import com.google.caliper.Param;
import htsjdk.samtools.Cigar;
import htsjdk.samtools.CigarElement;
import htsjdk.samtools.SAMFileReader;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.util.CloseableIterator;
import java.io.File;
/**
* Created by IntelliJ IDEA.
* User: mhanna
* Date: Apr 22, 2011
* Time: 4:01:23 PM
* To change this template use File | Settings | File Templates.
*/
public class TheoreticalMinimaBenchmark extends ReadProcessingBenchmark {
@Param
private String bamFile;
@Param
private Integer maxReads;
@Override
public String getBAMFile() { return bamFile; }
@Override
public Integer getMaxReads() { return maxReads; }
public void timeIterateOverEachBase(int reps) {
System.out.printf("Processing " + inputFile);
for(int i = 0; i < reps; i++) {
SAMFileReader reader = new SAMFileReader(inputFile);
CloseableIterator<SAMRecord> iterator = reader.iterator();
long As=0,Cs=0,Gs=0,Ts=0;
while(iterator.hasNext()) {
SAMRecord read = iterator.next();
for(byte base: read.getReadBases()) {
switch(base) {
case 'A': As++; break;
case 'C': Cs++; break;
case 'G': Gs++; break;
case 'T': Ts++; break;
}
}
}
System.out.printf("As = %d; Cs = %d; Gs = %d; Ts = %d; total = %d%n",As,Cs,Gs,Ts,As+Cs+Gs+Ts);
iterator.close();
reader.close();
}
}
public void timeIterateOverCigarString(int reps) {
for(int i = 0; i < reps; i++) {
long matchMismatches = 0;
long insertions = 0;
long deletions = 0;
long others = 0;
SAMFileReader reader = new SAMFileReader(inputFile);
CloseableIterator<SAMRecord> iterator = reader.iterator();
while(iterator.hasNext()) {
SAMRecord read = iterator.next();
Cigar cigar = read.getCigar();
for(CigarElement cigarElement: cigar.getCigarElements()) {
int elementSize = cigarElement.getLength();
while(elementSize > 0) {
switch(cigarElement.getOperator()) {
case M: case EQ: case X: matchMismatches++; break;
case I: insertions++; break;
case D: deletions++; break;
default: others++; break;
}
elementSize--;
}
}
}
System.out.printf("Ms = %d; Is = %d; Ds = %d; others = %d; total = %d%n",matchMismatches,insertions,deletions,others,matchMismatches+insertions+deletions+others);
iterator.close();
reader.close();
}
}
}