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package var2;
import java.util.HashSet;
import fileIO.ReadWrite;
import shared.Parse;
import shared.Tools;
import stream.SamLine;
public class SamFilter {
public boolean parse(String arg, String a, String b){
if(a.equals("min") || a.equals("minpos")){
minPos=Parse.parseIntKMG(b);
assert(minPos<=maxPos) : "minPos>maxPos";
}else if(a.equals("max") || a.equals("maxpos")){
maxPos=Parse.parseIntKMG(b);
assert(minPos<=maxPos) : "minPos>maxPos";
}else if(a.equals("minreadmapq") || a.equals("minsammapq") || a.equals("minmapq")){
minMapq=Parse.parseIntKMG(b);
}else if(a.equals("maxreadmapq") || a.equals("maxsammapq") || a.equals("maxmapq")){
maxMapq=Parse.parseIntKMG(b);
}else if(a.equals("mapped")){
includeMapped=Parse.parseBoolean(b);
}else if(a.equals("unmapped")){
includeUnmapped=Parse.parseBoolean(b);
}else if(a.equals("secondary") || a.equals("nonprimary")){
includeNonPrimary=Parse.parseBoolean(b);
}else if(a.equals("supplimentary")){
includeSupplimentary=Parse.parseBoolean(b);
}else if(a.equals("duplicate") || a.equals("duplicates")){
includeDuplicate=Parse.parseBoolean(b);
}else if(a.equals("qfail") || a.equals("samqfail")){
includeQfail=Parse.parseBoolean(b);
}else if(a.equals("lengthzero")){
includeLengthZero=Parse.parseBoolean(b);
}else if(a.equals("invert")){
invert=Parse.parseBoolean(b);
}else if(a.equals("minid")){
minId=Float.parseFloat(b);
if(minId>1f){minId/=100;}
assert(minId<=1f) : "minid should be between 0 and 1.";
}else if(a.equals("maxid")){
maxId=Float.parseFloat(b);
if(maxId>1f){maxId/=100;}
assert(maxId<=1f) : "maxid should be between 0 and 1.";
}else if(a.equals("contigs")){
addContig(b);
}else{
return false;
}
return true;
}
/*--------------------------------------------------------------*/
/*---------------- Filters ----------------*/
/*--------------------------------------------------------------*/
void addContig(String s){
if(s==null){return;}
if(s.indexOf(',')>=0){
for(String s2 : s.split(",")){
addContig(s2);
}
}
if(contigs==null){contigs=new HashSet<String>();}
contigs.add(s);
if(s.indexOf('_')>=0){addContig(s.replace('_', ' '));}
String[] split=s.split("\\s+");
if(split.length>0 && !split[0].equals(s)){contigs.add(split[0]);}
}
public boolean passesFilter(SamLine sl){
if(sl==null){return false;}
return invert^matchesFilter(sl);
}
boolean matchesFilter(SamLine sl){
if(sl==null){return false;}
if(!includeLengthZero && sl.length()<1){return false;}
if(!sl.mapped()){return includeUnmapped;}
else if(!includeMapped){return false;}
if(!includeNonPrimary && !sl.primary()){return false;}
if(!includeSupplimentary && sl.supplementary()){return false;}
if(!includeDuplicate && sl.duplicate()){return false;}
if(minPos>Integer.MIN_VALUE || maxPos<Integer.MAX_VALUE){
final int start=sl.start(true, false);
final int stop=sl.stop(start, true, false);
if(!Tools.overlap(start, stop, minPos, maxPos)){return false;}
}
if(minMapq>Integer.MIN_VALUE || maxMapq<Integer.MAX_VALUE){
if(sl.mapq>maxMapq || sl.mapq<minMapq){return false;}
}
if(sl.cigar!=null && (minId>0 || maxId<1)){
float identity=sl.calcIdentity();
if(identity<minId || identity>maxId){return false;}
}
if(contigs!=null){
String rname=sl.rnameS();
if(rname==null){return false;}
return contigs.contains(rname);
}
return true;
}
public boolean passesFilter(VCFLine vl){
if(vl==null){return false;}
return invert^matchesFilter(vl);
}
boolean matchesFilter(VCFLine vl){
if(vl==null){return false;}
if(minPos>Integer.MIN_VALUE || maxPos<Integer.MAX_VALUE){
final int start=vl.pos-1;
final int stop=start+(Tools.max(0, vl.reflen-1));
if(!Tools.overlap(start, stop, minPos, maxPos)){return false;}
}
if(contigs!=null){
String rname=vl.scaf;
if(rname==null){return false;}
return contigs.contains(rname);
}
return true;
}
public boolean passesFilter(Var v, ScafMap map){
if(v==null){return false;}
return invert^matchesFilter(v, map);
}
boolean matchesFilter(Var v, ScafMap map){
if(v==null){return false;}
if(minPos>Integer.MIN_VALUE || maxPos<Integer.MAX_VALUE){
final int start=v.start;
final int stop=v.stop;
if(!Tools.overlap(start, stop, minPos, maxPos)){return false;}
}
if(contigs!=null){
String rname=map.getName(v.scafnum);
if(rname==null){return false;}
return contigs.contains(rname);
}
return true;
}
public boolean passesFilter(String name){
if(name==null){return false;}
return invert^matchesFilter(name);
}
boolean matchesFilter(String name){
if(name==null){return false;}
if(contigs!=null){
return contigs.contains(name);
}
return true;
}
public void clear() {
minMapq=Integer.MIN_VALUE;
maxMapq=Integer.MAX_VALUE;
}
public int minPos=Integer.MIN_VALUE;
public int maxPos=Integer.MAX_VALUE;
public int minMapq=Integer.MIN_VALUE;
public int maxMapq=Integer.MAX_VALUE;
public float minId=Integer.MIN_VALUE;
public float maxId=Integer.MAX_VALUE;
public boolean includeUnmapped=true;
public boolean includeMapped=true;
public boolean includeSupplimentary=true;
public boolean includeQfail=false;
public boolean includeDuplicate=true;
public boolean includeNonPrimary=false;
public boolean includeLengthZero=false;
public HashSet<String> contigs=null;
public boolean invert=false;
public void setSamtoolsFilter(){
ReadWrite.SAMTOOLS_IGNORE_FLAG=0;
if(!includeUnmapped){ReadWrite.SAMTOOLS_IGNORE_FLAG|=ReadWrite.SAM_UNMAPPED;}
if(!includeNonPrimary){ReadWrite.SAMTOOLS_IGNORE_FLAG|=ReadWrite.SAM_SECONDARY;}
if(!includeSupplimentary){ReadWrite.SAMTOOLS_IGNORE_FLAG|=ReadWrite.SAM_SUPPLIMENTARY;}
if(!includeQfail){ReadWrite.SAMTOOLS_IGNORE_FLAG|=ReadWrite.SAM_QFAIL;}
if(!includeDuplicate){ReadWrite.SAMTOOLS_IGNORE_FLAG|=ReadWrite.SAM_QFAIL;}
}
/*--------------------------------------------------------------*/
}
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