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package barcode;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.Map.Entry;
import fileIO.ByteStreamWriter;
import shared.Tools;
import stream.Read;
import structures.ByteBuilder;
public class BarcodeMappingStats {
/*--------------------------------------------------------------*/
/*---------------- Constructor ----------------*/
/*--------------------------------------------------------------*/
public BarcodeMappingStats() {}
/*--------------------------------------------------------------*/
/*---------------- Methods ----------------*/
/*--------------------------------------------------------------*/
public void merge(BarcodeMappingStats bs) {
for(Entry<String, Barcode> e : bs.codeMap.entrySet()) {
Barcode b=e.getValue();
incrementCodeMap(b.name, b.count());
}
for(Entry<String, HashMap<String, Barcode>> e : bs.sourceMap.entrySet()) {
final String readKey=e.getKey();
final HashMap<String, Barcode> map=e.getValue();
for(Entry<String, Barcode> ee : map.entrySet()) {
final Barcode b=ee.getValue();
final String refKey=ee.getKey();
incrementSourceMap(readKey, refKey, b.count());
}
}
}
public void increment(Read r, String refKey){
String barcode=r.barcode(true);
incrementCodeMap(barcode, r.pairCount());
incrementSourceMap(barcode, refKey==null ? "UNKNOWN" : refKey, r.pairCount());
}
public void incrementCodeMap(String key, long amt) {
Barcode b=codeMap.get(key);
if(b==null){
b=new Barcode(key);
codeMap.put(key, b);
}
b.increment(amt);
}
public void incrementSourceMap(String readKey, String refKey, long amt) {
HashMap<String, Barcode> map=sourceMap.get(readKey);
if(map==null){
map=new HashMap<String, Barcode>();
sourceMap.put(readKey, map);
}
Barcode b=map.get(refKey);
if(b==null){
b=new Barcode(refKey);
map.put(refKey, b);
}
b.increment(amt);
}
public void writeStats(String outbarcodes, boolean overwrite) {
ByteBuilder bb=new ByteBuilder();
ArrayList<Barcode> codeList=toSortedList(codeMap);
final long sum=sum(codeList);
final double invSum=1.0/(Tools.max(1, sum));
ByteStreamWriter bsw=new ByteStreamWriter(outbarcodes, overwrite, false, true);
bsw.start();
bsw.println("#Reads\t"+sum);
bsw.println("#Barcode\tSource\tCount\tFraction");
for(Barcode bc : codeList) {
HashMap<String, Barcode> map=sourceMap.get(bc.name);
ArrayList<Barcode> sourceList=toSortedList(map);
final long sum2=sum(sourceList);
final double invSum2=1.0/(Tools.max(1, sum2));
for(Barcode source : sourceList) {
bb.append(bc.name).tab().append(source.name).tab().append(source.count()).tab().append(source.count()*invSum2, 6).nl();
bsw.print(bb);
bb.clear();
}
}
errorState|=bsw.poisonAndWait();
}
private static long sum(ArrayList<Barcode> list) {
long sum=0;
for(Barcode bc : list) {
sum+=bc.count();
}
return sum;
}
private static ArrayList<Barcode> toSortedList(HashMap<String, Barcode> map){
if(map==null || map.isEmpty()){return null;}
ArrayList<Barcode> list=new ArrayList<Barcode>(map.size());
for(Entry<String, Barcode> e : map.entrySet()) {
list.add(e.getValue());
}
Collections.sort(list);
return list;
}
/*--------------------------------------------------------------*/
/*---------------- Fields ----------------*/
/*--------------------------------------------------------------*/
/** Raw counts of barcodes */
public HashMap<String, Barcode> codeMap=new HashMap<String, Barcode>();
/**
* A table of tables. Key1 is the barcode of a read; key2 is where the read mapped to.
* The barcode for key2 tracks the number of times reads with key1 barcode mapped to key2's reference.
* E.G. if key1 is ABC-DEF then the top barcode in its table would be expected to
* be ABC-DEF, and other entries would indicate contamination of that library.
*
*/
public HashMap<String, HashMap<String, Barcode>> sourceMap=new HashMap<String, HashMap<String, Barcode>>();
public boolean errorState=false;
}
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