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package stream;
import dna.AminoAcid;
import shared.Tools;
/**
* @author Brian Bushnell
* @date May 5, 2016
*
*
*/
public class MDWalker {
MDWalker(String tag, String cigar_, byte[] longmatch_, SamLine sl_){//SamLine is just for debugging
mdTag=tag;
cigar=cigar_;
longmatch=longmatch_;
sl=sl_;
mdPos=(mdTag.startsWith("MD:Z:") ? 5 : 0);
matchPos=0;
bpos=0;
rpos=0;
sym=0;
current=0;
mode=0;
while(longmatch[matchPos]=='C'){
matchPos++;
bpos++;
}
}
void fixMatch(byte[] bases){
final boolean cigarContainsN=(cigar==null || cigar.indexOf('N')>=0);
sym=0;
while(mdPos<mdTag.length()){
char c=mdTag.charAt(mdPos);
mdPos++;
if(Tools.isDigit(c)){
current=(current*10)+(c-'0');
mode=NORMAL;
}else{
int matchPos2=matchPos;
if(current>0){
matchPos2=matchPos+current;
// System.err.println(mpos+", "+current+", "+mpos2);
assert(mode==NORMAL) : mode+", "+current;
current=0;
}
//Fixes subs after dels getting ignored
if(mode==DEL && (matchPos<longmatch.length && longmatch[matchPos]!='D')){
mode=SUB;
}
while(matchPos<matchPos2 || (matchPos<longmatch.length && (longmatch[matchPos]=='I' || false))){
assert(matchPos<longmatch.length) : longmatch.length+"\n"+sl.toString()+"\n"+new String(longmatch);
if(longmatch[matchPos]=='I'){
// System.err.println("I: mpos="+mpos+", bpos="+bpos);
matchPos2++;
bpos++;
matchPos++;
}else if(longmatch[matchPos]=='D'){//This should only happen if the cigar string contains an 'N'
assert(cigarContainsN) : matchPos+"\n"+new String(longmatch)+"\n"+mdTag+"\n"+cigar;
// System.err.println("M: mpos="+mpos+", bpos="+bpos);
while(longmatch[matchPos]=='D' && matchPos<longmatch.length){
rpos++;
matchPos++;
}
}else{
// System.err.println("M: mpos="+mpos+", bpos="+bpos);
rpos++;
bpos++;
matchPos++;
}
}
// while(mpos<longmatch.length && longmatch[mpos]=='I'){
// System.err.println("I2: mpos="+mpos+", bpos="+bpos);
// mpos++;
// bpos++;
// }
if(c=='^'){
mode=DEL;
// System.err.println("c="+((char)c)+", mpos="+mpos+", rpos="+rpos+", bpos="+bpos+", mode="+mode+(mode==NORMAL ? "" : ", match="+(char)longmatch[mpos-1])+"\n"+new String(longmatch));
}else if(mode==DEL){
// System.err.println("c="+((char)c)+", mpos="+mpos+", rpos="+rpos+", bpos="+bpos+", mode="+mode+(mode==NORMAL ? "" : ", match="+(char)longmatch[mpos-1])+"\n"+new String(longmatch));
rpos++;
matchPos++;
sym=c;
}
// else if(longmatch[mpos]=='I'){
// mode=INS;
// bpos++;
// mpos++;
// sym=c;
// }
else if(mode==NORMAL || mode==SUB){
if(longmatch[matchPos]=='D'){
assert(cigarContainsN) : matchPos+"\n"+new String(longmatch)+"\n"+mdTag+"\n"+cigar;
while(longmatch[matchPos]=='D' && matchPos<longmatch.length){
rpos++;
matchPos++;
}
}
assert(longmatch[matchPos]!='D') : matchPos+"\n"+new String(longmatch)+"\n"+mdTag+"\n"+cigar;
longmatch[matchPos]=(byte)'S';
if((bases!=null && !AminoAcid.isFullyDefined(bases[bpos])) || !AminoAcid.isFullyDefined(c)){longmatch[matchPos]='N';}
mode=SUB;
// System.err.println("c="+((char)c)+", mpos="+mpos+", rpos="+rpos+", bpos="+bpos+", mode="+mode+(mode==NORMAL ? "" : ", match="+(char)longmatch[mpos-1])+"\n"+new String(longmatch));
bpos++;
rpos++;
matchPos++;
sym=c;
}else{
assert(false);
}
}
}
// System.err.println();
// assert((bases==null || Read.calcMatchLength(longmatch)==bases.length)) :
// bases.length+", "+Read.calcMatchLength(longmatch)+"\n"+new String(longmatch)+"\n"
// + new String(Read.toShortMatchString(longmatch))+"\n"+mdTag;
}
boolean nextSub(){
sym=0;
while(mdPos<mdTag.length()){
char c=mdTag.charAt(mdPos);
mdPos++;
if(Tools.isDigit(c)){
current=(current*10)+(c-'0');
mode=NORMAL;
}else{
if(current>0){
bpos+=current;
rpos+=current;
matchPos+=current;
assert(mode==NORMAL) : mode+", "+current;
current=0;
}
if(c=='^'){mode=DEL;}
else if(mode==DEL){
rpos++;
matchPos++;
sym=c;
}else if(longmatch[matchPos]=='I'){
mode=INS;
bpos++;
matchPos++;
sym=c;
}else if(mode==NORMAL || mode==SUB || mode==INS){
mode=SUB;
bpos++;
rpos++;
matchPos++;
sym=c;
// System.err.println("c="+((char)c)+", mpos="+mpos+", rpos="+rpos+", bpos="+bpos+", mode="+mode+(mode==NORMAL ? "" : ", match="+(char)longmatch[mpos-1])+"\n"+new String(longmatch));
return true;
}
}
// System.err.println("c="+((char)c)+", mpos="+mpos+", rpos="+rpos+", bpos="+bpos+", mode="+mode+(mode==NORMAL ? "" : ", match="+(char)longmatch[mpos-1])+"\n"+new String(longmatch));
}
return false;
}
public int matchPosition(){
return matchPos-1;
}
public int basePosition(){
return bpos-1;
}
public int refPosition(){
return rpos-1;
}
public char symbol(){
assert(sym!=0);
return sym;
}
/** Position in match string (excluding clipping and insertions) */
private int matchPos;
/** Position in read bases (excluding clipping and insertions) */
private int bpos;
/** Position in reference bases (excluding clipping) */
private int rpos;
private char sym;
private String mdTag;
private String cigar; //Optional; for debugging
private byte[] longmatch;
private int mdPos;
private int current;
private int mode;
private SamLine sl;
// private int dels=0, subs=0, normals=0;
private static final int NORMAL=0, SUB=1, DEL=2, INS=3;
}
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