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package hiseq;
import shared.LineParser;
import shared.LineParserS3;
import structures.ByteBuilder;
/**
* Faster version of IlluminaHeaderParser using LineParser.
* @author Brian Bushnell
* @date April 3, 2024
*
*/
public class IlluminaHeaderParser2 extends ReadHeaderParser {
/*--------------------------------------------------------------*/
/*---------------- Expected Format ----------------*/
/*--------------------------------------------------------------*/
//@VP2-06:112:H7LNDMCVY:2:2437:14181:20134 (Novaseq6k)
//2402:6:1101:6337:2237/1
//MISEQ08:172:000000000-ABYD0:1:1101:18147:1925 1:N:0:TGGATATGCGCCAATT
//HISEQ07:419:HBFNEADXX:1:1101:1238:2072
//A00178:38:H5NYYDSXX:2:1101:3007:1000 1:N:0:CAACCTA+CTAGGTT
//@LH00223:28:22GLGMLT3:1:1101:5928:1016 1:N:0:CTGCTTGGTT+CTAACGACAG (NovaseqX)
// @HWI-Mxxxx or @Mxxxx - MiSeq
// @HWUSI - GAIIx
// @HWI-Dxxxx - HiSeq 2000/2500
// @Kxxxx - HiSeq 3000(?)/4000
// @Nxxxx - NextSeq 500/550
// @Axxxxx - NovaSeq
// @Vxxxxx = NextSeq 2000
// @AAxxxxx - NextSeq 2000 P1/P2/P3
// @Hxxxxxx - NovaSeq S1/S2/S4
//
// AAXX = Genome Analyzer
// BCXX = HiSeq v1.5
// ACXX = HiSeq High-Output v3
// ANXX = HiSeq High-Output v4
// ADXX = HiSeq RR v1
// AMXX, BCXX =HiSeq RR v2
// ALXX = HiSeqX
// BGXX, AGXX = High-Output NextSeq
// AFXX = Mid-Output NextSeq
// 5 letter/number = MiSeq
/*--------------------------------------------------------------*/
/*---------------- Main ----------------*/
/*--------------------------------------------------------------*/
public static void main(String[] args) {
IlluminaHeaderParser2 ihp=new IlluminaHeaderParser2();
ihp.test(args.length>0 ? args[0] : null);
}
/*--------------------------------------------------------------*/
/*---------------- Public Methods ----------------*/
/*--------------------------------------------------------------*/
public IlluminaHeaderParser2 parse(String id_) {
id=id_;
lp.set(id_);
whitespaceIndex=lp.indexOfWhitespace();
return this;
}
public boolean canShrink() {
return looksValid() && !looksShrunk();
}
public boolean looksValid() {
return(lp.terms()>=8 && whitespaceIndex>=6 && whitespaceIndex<=7);
}
public boolean looksShrunk() {
return(lp.terms()>3 && lp.bounds().get(2)==2);
}
@Override
public String machine() {
return lp.terms()<=0 ? null : lp.parseString(0);
}
@Override
public String sample() {
return null;
}
@Override
public int run() {
return lp.parseInt(1);
}
@Override
public String flowcell() {
return lp.parseString(2);
}
@Override
public int lane() {return lp.parseInt(3);}
@Override
public int tile() {return lp.parseInt(4);}
@Override
public int xPos() {return lp.parseInt(5);}
@Override
public int yPos() {return lp.parseInt(6);}
@Override
public char pairCode() {return lp.parseChar(whitespaceIndex+1, 0);}
@Override
public char chastityCode() {return lp.parseChar(whitespaceIndex+2, 0);}
@Override
public int controlBits() {return lp.parseInt(whitespaceIndex+3);}
@Override
public String barcode() {
return lp.terms()<=whitespaceIndex+4 ? null : lp.parseString(whitespaceIndex+4);
}
@Override
public String index3() {
return whitespaceIndex<7 ? null : lp.parseString(7);
}
@Override
public int whitespaceIndex() {
return whitespaceIndex;
}
@Override
public String extra() {
return lp.terms()<=whitespaceIndex+5 ? null : lp.parseString(whitespaceIndex+5);
}
public ByteBuilder appendTerm(ByteBuilder bb, int term) {
return lp.appendTerm(bb, term);
}
public ByteBuilder appendCoordinates(ByteBuilder bb) {
return bb.append(lane()).colon().append(tile()).colon()
.append(xPos()).colon().append(yPos());
}
public long encodeCoordinates() {
long x=lane();
x=(x<<17)^tile();
x=(x<<20)^xPos();
x=(x<<20)^yPos();
return x;
}
/*--------------------------------------------------------------*/
/*---------------- Private Fields ----------------*/
/*--------------------------------------------------------------*/
private final LineParserS3 lp=new LineParserS3(':');
public LineParser lp() {return lp;}
int whitespaceIndex=-1;
}
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