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package hiseq;
import shared.LineParserS4Reverse;
import structures.ByteBuilder;
/**
* Uses a reverse parser because BGI headers have an unknown prefix.
* As a result, it does not support comments, but this could be preprocessed.
* @author Brian Bushnell
* @date May 6, 2024
*
*/
public class BGIHeaderParser2 extends ReadHeaderParser {
/*--------------------------------------------------------------*/
/*---------------- Main ----------------*/
/*--------------------------------------------------------------*/
public static void main(String[] args) {
BGIHeaderParser2 ihp=new BGIHeaderParser2();
ihp.test(args.length>0 ? args[0] : null);
ihp.parse(args[0]);
System.err.println("toIllumina: "+ihp.toIllumina("ACGTACGT"));
}
/*--------------------------------------------------------------*/
/*---------------- Expected Format ----------------*/
/*--------------------------------------------------------------*/
//v300056266_run28L3C001R0010057888/1
//20A_V100002704L1C001R012000000/1
//E200008112L1C001R00100063962/1
//split: [v300056266, run28, 3, 001, 0010057888, 1]
/*--------------------------------------------------------------*/
/*---------------- Public Methods ----------------*/
/*--------------------------------------------------------------*/
public BGIHeaderParser2 parse(String id_) {
id=id_;
extra=null;
if(PARSE_EXTRA) {//Handles comments, but it's slow
int idx=firstWhitespace(id);
if(idx>=0) {
extra=id.substring(idx+1);
id=id.substring(0, idx);
}
}
lp.set(id);
return this;
}
private static int firstWhitespace(String s) {
for(int i=0; i<s.length(); i++) {
if(Character.isWhitespace(s.charAt(i))){
return i;
}
}
return -1;
}
//@LH00223:28:22GLGMLT3:1:1101:5928:1016 1:N:0:CTGCTTGGTT+CTAACGACAG (NovaseqX)
public String toIllumina(String barcode) {
bb.clear();
bb.append(machine()).colon();
bb.append(run()).colon();
bb.append(flowcell()).colon();
bb.append(lane()).colon();
bb.append(tile()).colon();
bb.append(xPos()).colon();
bb.append(yPos()).space();
bb.append(pairCode()).colon();
bb.append('N').colon();
bb.append(controlBits()).colon();
if(barcode!=null) {bb.append(barcode);}
String ex=extra();
if(ex!=null) {bb.tab().append(ex);}
return bb.toString();
}
@Override
public String sample() {
String s=lp.terms()<=1 ? null : lp.parseString(1);
return s!=null ? s : "SA";
}
@Override
public String machine() {
return "CG";//Complete Genomics
}
@Override
public int run() {
return 0;
}
@Override
public String flowcell() {
String s=lp.terms()<=0 ? null : lp.parseString(0);
// String s=lp.terms()<=1 ? null : lp.parseString(1);
return s!=null ? s : "FC";
}
@Override
public int lane() {return lp.parseInt(2);}
@Override
public int tile() {return lp.parseInt(4, 3, 10);}
@Override
public int xPos() {return lp.parseInt(3);}
@Override
public int yPos() {return lp.parseInt(4, 0, 3);}
@Override
public char pairCode() {return lp.parseChar(5, 0);}
@Override
public char chastityCode() {return 'N';}
@Override
public int controlBits() {return 0;}
@Override
public String barcode() {
return null;
}
@Override
public String extra() {
// return lp.terms()<=6 ? null : lp.parseString(6);
return extra;
}
/*--------------------------------------------------------------*/
/*---------------- Private Fields ----------------*/
/*--------------------------------------------------------------*/
private String extra=null;
private final LineParserS4Reverse lp=new LineParserS4Reverse("_LCR/");
private final ByteBuilder bb=new ByteBuilder(64);
/*--------------------------------------------------------------*/
/*---------------- Static Fields ----------------*/
/*--------------------------------------------------------------*/
public static boolean PARSE_EXTRA=false;
}
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