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package align2;
import java.io.File;
import java.util.Arrays;
import java.util.BitSet;
import dna.Data;
import fileIO.TextFile;
import shared.KillSwitch;
import shared.Parse;
import shared.PreParser;
import shared.Tools;
import stream.Read;
import stream.SamLine;
import stream.SiteScore;
/** Generate a file containing reads mapped correctly in one file and incorrectly in another file. */
public class CompareSamFiles {
public static void main(String[] args){
{//Preparse block for help, config files, and outstream
PreParser pp=new PreParser(args, new Object() { }.getClass().getEnclosingClass(), false);
args=pp.args;
//outstream=pp.outstream;
}
String in1=null;
String in2=null;
long reads=-1;
for(int i=0; i<args.length; i++){
final String arg=args[i];
final String[] split=arg.split("=");
String a=split[0].toLowerCase();
String b=split.length>1 ? split[1] : null;
if(a.equals("path") || a.equals("root")){
Data.setPath(b);
}else if(a.equals("in") || a.equals("in1")){
in1=b;
}else if(a.equals("in2")){
in2=b;
}else if(a.equals("parsecustom")){
parsecustom=Parse.parseBoolean(b);
}else if(a.equals("thresh")){
THRESH2=Integer.parseInt(b);
}else if(a.equals("printerr")){
printerr=Parse.parseBoolean(b);
// }else if(a.equals("ssaha2") || a.equals("subtractleadingclip")){
// SamLine.SUBTRACT_LEADING_SOFT_CLIP=Parse.parseBoolean(b);
}else if(a.equals("blasr")){
BLASR=Parse.parseBoolean(b);
}else if(a.equals("q") || a.equals("quality") || a.startsWith("minq")){
minQuality=Integer.parseInt(b);
}else if(in1==null && i==0 && args[i].indexOf('=')<0 && (a.startsWith("stdin") || new File(args[i]).exists())){
in1=args[i];
}else if(in2==null && i==1 && args[i].indexOf('=')<0 && (a.startsWith("stdin") || new File(args[i]).exists())){
in2=args[i];
}else if(a.equals("reads")){
reads=Parse.parseKMG(b);
}else if(i==2 && args[i].indexOf('=')<0 && Tools.isDigit(a.charAt(0))){
reads=Parse.parseKMG(a);
}
}
assert(in1!=null) : args[0]+".exists() ? "+new File(args[0]).exists();
// assert(in2!=null) : args[1]+".exists() ? "+new File(args[1]).exists();
if(reads<1){
// assert(false) : "Number of expected reads was not specified. Please add a parameter reads=<number> or disable assertions.";
reads=100000;
System.err.println("Warning - number of expected reads was not specified.");
}
TextFile tf1=new TextFile(in1, false);
TextFile tf2=null;
if(in2!=null){tf2=new TextFile(in2, false);}
BitSet truePos1=new BitSet((int)reads);
BitSet falsePos1=new BitSet((int)reads);
BitSet truePos2=new BitSet((int)reads);
BitSet falsePos2=new BitSet((int)reads);
String s=null;
TextFile tf;
{
tf=tf1;
for(s=tf.nextLine(); s!=null; s=tf.nextLine()){
char c=s.charAt(0);
if(c!='@'/* && c!=' ' && c!='\t'*/){
SamLine sl=new SamLine(s);
if(sl.primary()){
Read r=sl.toRead(parsecustom);
if(parsecustom && r.originalSite==null){
assert(false);
System.err.println("Turned off custom parsing.");
parsecustom=false;
}
//System.out.println(r);
int type=type(r, sl);
int id=(int)r.numericID;
if(type==2){truePos1.set(id);}
else if(type>2){falsePos1.set(id);}
}
}
}
tf.close();
}
if(tf2!=null){
tf=tf2;
for(s=tf.nextLine(); s!=null; s=tf.nextLine()){
char c=s.charAt(0);
if(c!='@'/* && c!=' ' && c!='\t'*/){
SamLine sl=new SamLine(s);
if(sl.primary()){
Read r=sl.toRead(parsecustom);
if(parsecustom && r.originalSite==null){
assert(false);
System.err.println("Turned off custom parsing.");
parsecustom=false;
}
//System.out.println(r);
int type=type(r, sl);
int id=(int)r.numericID;
if(type==2){truePos2.set(id);}
else if(type>2){falsePos2.set(id);}
}
}
}
tf.close();
}
BitSet added=new BitSet((int)reads);
{
tf=tf1;
tf.reset();
for(s=tf.nextLine(); s!=null; s=tf.nextLine()){
char c=s.charAt(0);
if(c!='@'/* && c!=' ' && c!='\t'*/){
SamLine sl=new SamLine(s);
// assert(false) : s+", "+truePos1.cardinality()+", "+truePos2.cardinality()+", "+falsePos1.cardinality()+", "+falsePos2.cardinality()+", ";
if(sl.primary()){
Read r=sl.toRead(parsecustom);
int id=(int)r.numericID;
if(!added.get(id)){
// if(truePos1.get(id)!=truePos2.get(id) || falsePos1.get(id)!=falsePos2.get(id)){
// System.out.println(s);
// added.set(id);
// }
// if(falsePos1.get(id) && truePos2.get(id)){
// System.out.println(s);
// added.set(id);
// }
if(falsePos1.get(id) && !falsePos2.get(id)){
System.out.println(s);
added.set(id);
}
}
}
}
}
tf.close();
}
if(tf2!=null){
tf=tf2;
tf.reset();
for(s=tf.nextLine(); s!=null; s=tf.nextLine()){
char c=s.charAt(0);
if(c!='@'/* && c!=' ' && c!='\t'*/){
SamLine sl=new SamLine(s);
if(sl.primary()){
Read r=sl.toRead(parsecustom);
int id=(int)r.numericID;
if(!added.get(id)){
// if(truePos1.get(id)!=truePos2.get(id) || falsePos1.get(id)!=falsePos2.get(id)){
// System.out.println(s);
// added.set(id);
// }
// if(falsePos2.get(id) && truePos1.get(id)){
// System.out.println(s);
// added.set(id);
// }
if(falsePos2.get(id) && !falsePos1.get(id)){
System.out.println(s);
added.set(id);
}
}
}
}
}
tf.close();
}
}
public static void calcStatistics1(final Read r, SamLine sl){
int THRESH=0;
primary++;
if(r.discarded()/* || r.mapScore==0*/){
discarded++;
unmapped++;
}else if(r.ambiguous()){
// assert(r.mapped()) : "\n"+r+"\n"+sl+"\n";
if(r.mapped()){mapped++;}
ambiguous++;
}else if(r.mapScore<1){
unmapped++;
}else if(r.mapScore<=minQuality){
if(r.mapped()){mapped++;}
ambiguous++;
}else{
if(!r.mapped()){
unmapped++;
}else{
mapped++;
mappedRetained++;
if(parsecustom){
SiteScore os=r.originalSite;
assert(os!=null);
if(os!=null){
int trueChrom=os.chrom;
byte trueStrand=os.strand;
int trueStart=os.start;
int trueStop=os.stop;
SiteScore ss=new SiteScore(r.chrom, r.strand(), r.start, r.stop, 0, 0);
byte[] originalContig=sl.originalContig();
if(BLASR){
originalContig=(originalContig==null || Tools.indexOf(originalContig, (byte)'/')<0 ? originalContig :
KillSwitch.copyOfRange(originalContig, 0, Tools.lastIndexOf(originalContig, (byte)'/')));
}
int cstart=sl.originalContigStart();
boolean strict=isCorrectHit(ss, trueChrom, trueStrand, trueStart, trueStop, THRESH, originalContig, sl.rname(), cstart);
boolean loose=isCorrectHitLoose(ss, trueChrom, trueStrand, trueStart, trueStop, THRESH+THRESH2, originalContig, sl.rname(), cstart);
// if(!strict){
// System.out.println(ss+", "+new String(originalContig)+", "+new String(sl.rname()));
// assert(false);
// }
// System.out.println("loose = "+loose+" for "+r.toText());
if(loose){
// System.err.println("TPL\t"+trueChrom+", "+trueStrand+", "+trueStart+", "+trueStop+"\tvs\t"
// +ss.chrom+", "+ss.strand+", "+ss.start+", "+ss.stop);
truePositiveLoose++;
}else{
// System.err.println("FPL\t"+trueChrom+", "+trueStrand+", "+trueStart+", "+trueStop+"\tvs\t"
// +ss.chrom+", "+ss.strand+", "+ss.start+", "+ss.stop);
falsePositiveLoose++;
}
if(strict){
// System.err.println("TPS\t"+trueStart+", "+trueStop+"\tvs\t"+ss.start+", "+ss.stop);
truePositiveStrict++;
}else{
// System.err.println("FPS\t"+trueStart+", "+trueStop+"\tvs\t"+ss.start+", "+ss.stop);
falsePositiveStrict++;
}
}
}
}
}
}
public static int type(final Read r, SamLine sl){
int THRESH=0;
primary++;
if(r.discarded()/* || r.mapScore==0*/){
return 0;
}else if(r.ambiguous()){
return 1;
}else if(r.mapScore<1){
return 0;
}else if(r.mapScore<=minQuality){
return 1;
}else{
if(!r.mapped()){
return 0;
}else{
if(parsecustom){
SiteScore os=r.originalSite;
assert(os!=null);
if(os!=null){
int trueChrom=os.chrom;
byte trueStrand=os.strand;
int trueStart=os.start;
int trueStop=os.stop;
SiteScore ss=new SiteScore(r.chrom, r.strand(), r.start, r.stop, 0, 0);
byte[] originalContig=sl.originalContig();
if(BLASR){
originalContig=(originalContig==null || Tools.indexOf(originalContig, (byte)'/')<0 ? originalContig :
KillSwitch.copyOfRange(originalContig, 0, Tools.lastIndexOf(originalContig, (byte)'/')));
}
int cstart=sl.originalContigStart();
boolean strict=isCorrectHit(ss, trueChrom, trueStrand, trueStart, trueStop, THRESH, originalContig, sl.rname(), cstart);
boolean loose=isCorrectHitLoose(ss, trueChrom, trueStrand, trueStart, trueStop, THRESH+THRESH2, originalContig, sl.rname(), cstart);
if(strict){return 2;}
if(loose){return 3;}
return 4;
}
}
}
}
return 0;
}
public static boolean isCorrectHit(SiteScore ss, int trueChrom, byte trueStrand, int trueStart, int trueStop, int thresh,
byte[] originalContig, byte[] contig, int cstart){
if(ss.strand!=trueStrand){return false;}
if(originalContig!=null){
if(!Arrays.equals(originalContig, contig)){return false;}
}else{
if(ss.chrom!=trueChrom){return false;}
}
assert(ss.stop>ss.start) : ss.toText()+", "+trueStart+", "+trueStop;
assert(trueStop>trueStart) : ss.toText()+", "+trueStart+", "+trueStop;
int cstop=cstart+trueStop-trueStart;
// return (absdif(ss.start, trueStart)<=thresh && absdif(ss.stop, trueStop)<=thresh);
return (absdif(ss.start, cstart)<=thresh && absdif(ss.stop, cstop)<=thresh);
}
public static boolean isCorrectHitLoose(SiteScore ss, int trueChrom, byte trueStrand, int trueStart, int trueStop, int thresh,
byte[] originalContig, byte[] contig, int cstart){
if(ss.strand!=trueStrand){return false;}
if(originalContig!=null){
if(!Arrays.equals(originalContig, contig)){return false;}
}else{
if(ss.chrom!=trueChrom){return false;}
}
assert(ss.stop>ss.start) : ss.toText()+", "+trueStart+", "+trueStop;
assert(trueStop>trueStart) : ss.toText()+", "+trueStart+", "+trueStop;
int cstop=cstart+trueStop-trueStart;
// return (absdif(ss.start, trueStart)<=thresh || absdif(ss.stop, trueStop)<=thresh);
return (absdif(ss.start, cstart)<=thresh || absdif(ss.stop, cstop)<=thresh);
}
private static final int absdif(int a, int b){
return a>b ? a-b : b-a;
}
public static int truePositiveStrict=0;
public static int falsePositiveStrict=0;
public static int truePositiveLoose=0;
public static int falsePositiveLoose=0;
public static int mapped=0;
public static int mappedRetained=0;
public static int unmapped=0;
public static int discarded=0;
public static int ambiguous=0;
public static long lines=0;
public static long primary=0;
public static long secondary=0;
public static int minQuality=3;
public static boolean parsecustom=true;
public static boolean printerr=false;
public static int THRESH2=20;
public static boolean BLASR=false;
}
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