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package jgi;
import java.util.Arrays;
import java.util.HashMap;
import shared.Tools;
/**
* @author Brian Bushnell
* @date Oct 10, 2014
*
*/
public class CovStatsLine {
public CovStatsLine(String s){
this(s.split("\t"));
}
/**
* ID Avg_fold Length Ref_GC Covered_percent Covered_bases Plus_reads Minus_reads (optional.... Read_GC)
* @param split
*/
public CovStatsLine(String[] split) {
assert(split.length>=8) : Arrays.toString(split);
assert(!split[0].startsWith("#")) : Arrays.toString(split);
assert(id_FNUM==0) : "Not initialized with header: "+id_FNUM;
if(id_FNUM>=0){id=split[id_FNUM];}
if(length_FNUM>=0){length=Integer.parseInt(split[length_FNUM]);}
if(coveredBases_FNUM>=0){coveredBases=Integer.parseInt(split[coveredBases_FNUM]);}
if(plusReads_FNUM>=0){plusReads=Long.parseLong(split[plusReads_FNUM]);}
if(minusReads_FNUM>=0){minusReads=Long.parseLong(split[minusReads_FNUM]);}
if(avgFold_FNUM>=0){avgFold=Double.parseDouble(split[avgFold_FNUM]);}
if(refGC_FNUM>=0){refGC=Double.parseDouble(split[refGC_FNUM]);}
if(median_FNUM>=0){median=Long.parseLong(split[median_FNUM]);}
if(underMin_FNUM>=0){underMin=Integer.parseInt(split[underMin_FNUM]);}
if(readGC_FNUM>=0){readGC=Double.parseDouble(split[readGC_FNUM]);}
if(stdDev_FNUM>=0){stdDev=Double.parseDouble(split[stdDev_FNUM]);}
// assert(split.length>=8) : Arrays.toString(split);
// assert(!split[0].startsWith("#")) : Arrays.toString(split);
// id=split[0];
// avgFold=Double.parseDouble(split[1]);
// length=Integer.parseInt(split[2]);
// refGC=Double.parseDouble(split[3]);
//// coveredPercent=Double.parseDouble(split[4]);
// coveredBases=Integer.parseInt(split[5]);
// plusReads=Long.parseLong(split[6]);
// minusReads=Long.parseLong(split[7]);
// if(split.length==11){
// median=Integer.parseInt(split[8]);
// underMin=Integer.parseInt(split[9]);
// readGC=Double.parseDouble(split[10]);
// }else if(split.length==10){
// median=Integer.parseInt(split[8]);
// if(CoveragePileup.USE_BITSETS && CoveragePileup.USE_WINDOW){
// underMin=Integer.parseInt(split[9]);
// }else{
// readGC=Double.parseDouble(split[9]);
// }
// }else if(split.length==9){
// readGC=Double.parseDouble(split[8]);
// }else if(split.length<9){
// //do nothing
// }
}
public final double coveredPercent(){
return (100.0*coveredBases)/Tools.max(1, length);
}
public final long reads(){return plusReads+minusReads;}
/**
* @param csl
*/
public void add(CovStatsLine csl) {
double invlen2=1d/Tools.max(1, length+csl.length);
avgFold=((avgFold*length)+(csl.avgFold*csl.length))*invlen2;
refGC=((refGC*length)+(csl.refGC*csl.length))*invlen2;
readGC=((readGC*reads())+(csl.readGC*csl.reads()))*1.0/(Tools.max(1, reads()+csl.reads()));
length+=csl.length;
coveredBases+=csl.coveredBases;
plusReads+=csl.plusReads;
minusReads+=csl.minusReads;
median=median+csl.median;
underMin=underMin+csl.underMin;
}
@Override
public String toString(){
return Tools.format("%s\t%.4f\t%d\t%.4f\t%.4f\t%d\t%d\t%d\t%d\t%d\t%.4f\t%.4f", id, avgFold, length,
refGC, coveredPercent(), coveredBases, plusReads, minusReads, median, underMin, readGC, stdDev);
}
public static void initializeHeader(String header){
while(header.startsWith("#")){header=header.substring(1);}
String[] split=header.split("\t");
HashMap<String, Integer> map=new HashMap<String, Integer>(23);
for(int i=0; i<split.length; i++){
String s=split[i].toLowerCase();
if(s.startsWith("under_")){s="under_min";}
map.put(split[i].toLowerCase(), i);
}
id_FNUM=map.containsKey("id") ? map.get("id") : -1;
avgFold_FNUM=map.containsKey("avg_fold") ? map.get("avg_fold") : -1;
length_FNUM=map.containsKey("length") ? map.get("length") : -1;
refGC_FNUM=map.containsKey("ref_gc") ? map.get("ref_gc") : -1;
coveredBases_FNUM=map.containsKey("covered_bases") ? map.get("covered_bases") : -1;
plusReads_FNUM=map.containsKey("plus_reads") ? map.get("plus_reads") : -1;
minusReads_FNUM=map.containsKey("minus_reads") ? map.get("minus_reads") : -1;
median_FNUM=map.containsKey("median_fold") ? map.get("median_fold") : -1;
underMin_FNUM=map.containsKey("under_min") ? map.get("under_min") : -1;
readGC_FNUM=map.containsKey("read_gc") ? map.get("read_gc") : -1;
stdDev_FNUM=map.containsKey("std_dev") ? map.get("std_dev") : -1;
assert(id_FNUM==0) : "Bad header: "+id_FNUM+"\n"+header+"\n"+map;
}
// public static final String header1="#ID\tAvg_fold\tLength\tRef_GC\tCovered_percent\tCovered_bases\tPlus_reads\tMinus_reads\tMedian_fold\tUnder_min\tRead_GC";
// public static final String header2="#ID\tAvg_fold\tLength\tRef_GC\tCovered_percent\tCovered_bases\tPlus_reads\tMinus_reads\tRead_GC";
public String id;
public int length;
public int coveredBases;
public long plusReads;
public long minusReads;
public double avgFold;
public double refGC;
public long median;
public int underMin;
public double readGC;
public double stdDev;
private static int id_FNUM=-1;
private static int length_FNUM=-1;
private static int coveredBases_FNUM=-1;
private static int plusReads_FNUM=-1;
private static int minusReads_FNUM=-1;
private static int avgFold_FNUM=-1;
private static int refGC_FNUM=-1;
private static int median_FNUM=-1;
private static int underMin_FNUM=-1;
private static int readGC_FNUM=-1;
private static int stdDev_FNUM=-1;
}
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