--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/gff/GffLine.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,389 @@
+package gff;
+
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.Locale;
+
+import dna.Data;
+import fileIO.ByteFile;
+import fileIO.FileFormat;
+import prok.ProkObject;
+import shared.Parse;
+import shared.Shared;
+import shared.Tools;
+import structures.ByteBuilder;
+import var2.ScafMap;
+import var2.VCFLine;
+import var2.Var;
+
+/**
+ * Used by both the var2 and prok packages for processing gff files.
+ * @author Brian Bushnell
+ * @date Sep 12, 2018
+ *
+ */
+public class GffLine {
+	
+	//#seqid	source	type	start	end	score	strand	phase	attributes
+	public GffLine(byte[] line){
+		int a=0, b=0;
+		
+		while(b<line.length && line[b]!='\t'){b++;}
+		assert(b>a) : "Missing field 0: "+new String(line);
+		seqid=parseSeqid ? intern(new String(line, a, b-a)) : null;
+//		assert(seqid==null || seqid.equals(new String(line, a, b-a)));
+//		assert(seqid!=null) : new String(line, a, b-a)+", "+a+", "+b+"\n"+line;
+		b++;
+		a=b;
+		
+		while(b<line.length && line[b]!='\t'){b++;}
+		assert(b>a) : "Missing field 1: "+new String(line);
+		if(b==a+1 && line[a]=='.'){source=DOTS;}
+		else{source=paseSource ? intern(new String(line, a, b-a)) : null;}
+		b++;
+		a=b;
+		
+		while(b<line.length && line[b]!='\t'){b++;}
+		assert(b>a) : "Missing field 2: "+new String(line);
+		if(b==a+1 && line[a]=='.'){type=DOTS;}
+		else{
+			try {//This was to catch a probably intermittent hardware error; can't replicate.
+				type=(parseType ? intern(new String(line, a, b-a)) : null);
+			} catch (Exception e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+				System.err.println("\n"+new String(line)+"\n"+a+", "+b+", "+(b-a));
+				assert(false);
+			}
+		}
+		b++;
+		a=b;
+		
+		while(b<line.length && line[b]!='\t'){b++;}
+		assert(b>a) : "Missing field 3: "+new String(line);
+		start=Parse.parseInt(line, a, b);
+		b++;
+		a=b;
+		
+		while(b<line.length && line[b]!='\t'){b++;}
+		assert(b>a) : "Missing field 4: "+new String(line);
+		stop=Parse.parseInt(line, a, b);
+		b++;
+		a=b;
+		
+		while(b<line.length && line[b]!='\t'){b++;}
+		if(b<=a){
+			//Badly formatted line; common in IMG
+			return;
+		}
+		assert(b>a) : "Missing field 5: "+new String(line);
+		if(b==a+1 && line[a]=='.'){score=-1;}
+		else{score=Parse.parseFloat(line, a, b);}
+		b++;
+		a=b;
+		
+		while(b<line.length && line[b]!='\t'){b++;}
+		assert(b>a) : "Missing field 6: "+new String(line);
+		assert(b==a+1);
+		strand=find(line[a], STRANDS);
+//		assert(strand>0) : line[a]+", "+Arrays.toString(STRANDS)+", "+(char)line[b];
+		b++;
+		a=b;
+		
+		while(b<line.length && line[b]!='\t'){b++;}
+		assert(b>a) : "Missing field 7: "+new String(line);
+		assert(b==a+1);
+		if(line[a]=='.'){phase=-1;}
+		else{phase=Parse.parseInt(line, a, b);}
+		b++;
+		a=b;
+		
+		while(b<line.length && line[b]!='\t'){b++;}
+		assert(b>a) : "Missing field 8: "+new String(line);
+		if(b==a+1 && line[a]=='.'){attributes=DOTS;}
+		else{attributes=parseAttributes ? new String(line, a, b-a) : null;}
+		b++;
+		a=b;
+		
+//		assert(strand>=0) : "\n"+this.toString()+"\n"+new String(line);
+	}
+	
+	public GffLine(VCFLine vcf){
+		seqid=vcf.scaf;
+		source=DOTS;
+		type="sequence_variant_obs";
+		start=vcf.start()+1;
+		stop=vcf.stop()+1;
+		score=(float)vcf.qual;
+		strand=PLUS;
+		phase=-1;
+		final int vtype=vcf.type();
+		ByteBuilder bb=new ByteBuilder(16);
+		bb.append("ID=").append(Var.typeArray[vtype]).append(' ');
+		if(vtype==Var.SUB){
+			bb.append(vcf.ref).append('>').append(vcf.alt);
+		}else if(vtype==Var.DEL){
+			bb.append("length ").append(vcf.reflen()-vcf.readlen());
+		}else if(vtype==Var.INS){
+			int offset=vcf.reflen();
+			int length=vcf.readlen()-offset;
+			bb.append(vcf.alt, offset, length);
+		}else if(vtype==Var.NOCALL){
+			bb.append("length ").append(vcf.reflen());
+		}
+		attributes=bb.toString();
+		bb.clear();
+	}
+	
+	public GffLine(Var v, double properPairRate, double totalQualityAvg, double totalMapqAvg, double readLengthAvg, double rarity, int ploidy, ScafMap map){
+		seqid=v.scafName();
+		source=DOTS;
+		type="sequence_variant_obs";
+		start=v.start+1;
+		stop=Tools.max(v.start+1, v.stop);
+		score=(float)v.score(properPairRate, totalQualityAvg, totalMapqAvg, readLengthAvg, rarity, ploidy, map);
+		strand=PLUS;
+		phase=-1;
+		final int vtype=v.type();
+		ByteBuilder bb=new ByteBuilder(16);
+		bb.append("ID=").append(Var.typeArray[vtype]);
+		if(vtype==Var.SUB || vtype==Var.INS){
+			bb.append(' ').append(v.allele);
+		}else if(vtype==Var.DEL || vtype==Var.NOCALL){
+			bb.append(" length ").append(v.reflen());
+		}else{assert(false) : vtype+"\n"+v;}
+		attributes=bb.toString();
+		bb.clear();
+	}
+	
+	public GffLine(Var v){
+		seqid=v.scafName();
+		source="BBTools";
+		type="sequence_variant_obs";
+		start=v.start+1;
+		stop=Tools.max(v.start+1, v.stop);
+		score=-1;
+		strand=PLUS;
+		phase=-1;
+		final int vtype=v.type();
+		ByteBuilder bb=new ByteBuilder(16);
+		bb.append("ID=").append(Var.typeArray[vtype]);
+		if(vtype==Var.SUB || vtype==Var.INS){
+			bb.append(' ').append(v.allele);
+		}else if(vtype==Var.DEL || vtype==Var.NOCALL){
+			bb.append(" length ").append(v.reflen());
+		}else{assert(false) : vtype+"\n"+v;}
+		attributes=bb.toString();
+		bb.clear();
+	}
+	
+	public static ArrayList<GffLine> loadGffFile(String fname, String types, boolean banUnprocessed){
+		FileFormat ff=FileFormat.testInput(fname, FileFormat.GFF, null, false, false);
+		return loadGffFile(ff, types, banUnprocessed);
+	}
+	
+	public static ArrayList<GffLine>[] loadGffFileByType(FileFormat ff, String types, boolean banUnprocessed){
+		ArrayList<GffLine> list=loadGffFile(ff, types, banUnprocessed);
+		String[] typeArray=types.split(",");
+		ArrayList<GffLine>[] lists=new ArrayList[typeArray.length];
+		for(int i=0; i<typeArray.length; i++){
+			String type=typeArray[i];
+			lists[i]=new ArrayList<GffLine>();
+			for(GffLine gline : list){
+				if(gline.type.equals(type)){
+					lists[i].add(gline);
+				}
+			}
+		}
+		return lists;
+	}
+	
+	public static ArrayList<GffLine> loadGffFile(FileFormat ff, String types, boolean banUnprocessed){
+		HashSet<String> set=null;
+		if(types!=null){
+			String[] split=types.split(",");
+			set=new HashSet<String>(split.length*2);
+			for(String s : split){
+				set.add(s);
+			}
+		}
+		
+		ArrayList<GffLine> list=new ArrayList<GffLine>();
+		ByteFile bf=ByteFile.makeByteFile(ff);
+		for(byte[] line=bf.nextLine(); line!=null; line=bf.nextLine()){
+			if(line[0]=='#'){
+				//skip
+			}else{
+				GffLine gline=new GffLine(line);
+				assert(gline.strand>=0) : "\n"+gline.toString()+"\n"+new String(line)+"\n";
+				if(set==null || (gline.type!=null && set.contains(gline.type))){
+					if(!banUnprocessed || ProkObject.processType(gline.prokType())){
+						list.add(gline);
+					}
+				}
+			}
+		}
+		
+		boolean error=bf.close();
+		assert(!error) : "Problem with file "+ff.name();
+		return list;
+	}
+	
+	public static void toText(ByteBuilder bb, Var v, double properPairRate, double totalQualityAvg, 
+			double totalMapqAvg, double readLengthAvg, double rarity, int ploidy, ScafMap map){
+//		assert(false);
+		bb.append(v.scafName(map)).append('\t');
+		bb.append('.').append('\t');
+		bb.append("sequence_variant_obs").append('\t');
+		bb.append(v.start+1).append('\t');
+		bb.append(Tools.max(v.start+1, v.stop)).append('\t');
+		bb.append(v.score(properPairRate, totalQualityAvg, totalMapqAvg, readLengthAvg, rarity, ploidy, map), 2).append('\t');
+		bb.append('+').append('\t');
+		bb.append('.').append('\t');
+//		System.err.println(v.typeString()+", "+v.start+", "+v.stop);
+		final int vtype=v.type();
+		bb.append("ID=").append(Var.typeArray[vtype]);
+		if(vtype==Var.SUB || vtype==Var.INS){
+			bb.append(' ').append(v.allele);
+		}else if(vtype==Var.DEL || vtype==Var.NOCALL){
+			bb.append(" length ").append(v.reflen());
+		}else{assert(false) : vtype+"\n"+v;}
+	}
+	
+	public static String toHeader(double properPairRate, double totalQualityAvg, double mapqAvg, double rarity, double minAlleleFraction, int ploidy, 
+			long reads, long pairs, long properPairs, long bases, String ref){
+		StringBuilder sb=new StringBuilder();
+		
+		final double readLengthAvg=bases/Tools.max(1.0, reads);
+		sb.append("##gff-version 3\n");
+		sb.append("#BBMapVersion\t"+Shared.BBMAP_VERSION_STRING+"\n");
+		sb.append("#ploidy\t"+ploidy+"\n");
+		sb.append(String.format(Locale.ROOT, "#rarity\t%.5f\n", rarity));
+		sb.append(String.format(Locale.ROOT, "#minAlleleFraction\t%.4f\n", minAlleleFraction));
+		sb.append("#reads\t"+reads+"\n");
+		sb.append("#pairedReads\t"+pairs+"\n");
+		sb.append("#properlyPairedReads\t"+properPairs+"\n");
+		sb.append(String.format(Locale.ROOT, "#readLengthAvg\t%.2f\n", readLengthAvg));
+		sb.append(String.format(Locale.ROOT, "#properPairRate\t%.4f\n", properPairRate));
+		sb.append(String.format(Locale.ROOT, "#totalQualityAvg\t%.4f\n", totalQualityAvg));
+		sb.append(String.format(Locale.ROOT, "#mapqAvg\t%.2f\n", mapqAvg));
+		if(ref!=null){sb.append("#reference\t"+ref+"\n");}
+		
+		sb.append("#seqid	source	type	start	end	score	strand	phase	attributes");
+		return sb.toString();
+	}
+	
+	@Override
+	public String toString(){
+		ByteBuilder bb=new ByteBuilder();
+		appendTo(bb);
+		return bb.toString();
+	}
+	
+	public ByteBuilder appendTo(ByteBuilder bb){
+		bb.append(seqid==null ? "." : seqid).append('\t');
+		bb.append(source==null ? "." : source).append('\t');
+		bb.append(type==null ? "." : type).append('\t');
+		bb.append(start).append('\t');
+		bb.append(stop).append('\t');
+		if(score<0){bb.append('.').append('\t');}
+		else{bb.append(score, 2).append('\t');}
+		
+		bb.append((strand>=0 ? STRANDS[strand] : (byte)'.')).append('\t');
+		
+		if(phase<0){bb.append('.').append('\t');}
+		else{bb.append(phase).append('\t');}
+		
+		bb.append(attributes==null ? "." : attributes);
+		return bb;
+	}
+	
+	public int length() {
+		return stop-start+1;
+	}
+	
+	private static int find(byte a, byte[] array){
+		for(int i=0; i<array.length; i++){
+			if(array[i]==a){return i;}
+		}
+		return -1;
+	}
+	
+	private static String intern(String s){
+		return Data.forceIntern(s);
+	}
+	
+	@Override
+	public int hashCode(){
+		return trueStop()^seqid.hashCode();
+	}
+	
+	@Override
+	public boolean equals(Object o){
+		GffLine b=(GffLine)o;
+		if(start!=b.start){return false;}
+		if(stop!=b.stop){return false;}
+		if(strand!=b.strand){return false;}
+		if(!seqid.equals(b.seqid)){return false;}
+		if(!type.equals(b.type)){return false;}
+		return true;
+	}
+	
+	public int trueStart(){
+		return strand==0 ? start : stop;
+	}
+	
+	public int trueStop(){
+		return strand==0 ? stop : start;
+	}
+	
+	public final int prokType(){
+		if(type.equals("CDS")){
+			return ProkObject.CDS;
+		}else if(type.equals("tRNA")){
+			return ProkObject.tRNA;
+		}else if(type.equals("rRNA")){
+			if(attributes.contains("16S")){
+				return ProkObject.r16S;
+			}else if(attributes.contains("23S")){
+				return ProkObject.r23S;
+			}else if(attributes.contains("18S")){
+				return ProkObject.r18S;
+			}else if(attributes.contains("5S") && length()<300){
+				return ProkObject.r5S;
+			}
+		}
+		return -1;
+	}
+	
+	public final boolean partial(){return attributes!=null && attributes.contains("partial=true");}
+	
+	public final boolean inbounds(int scaflen){return start>=0 && stop<scaflen;}
+	
+	public String seqid;
+	public String source;
+	public String type;
+	public int start;
+	public int stop;
+	public float score;
+	public int strand;
+	public int phase;
+	public String attributes;
+	
+	private static final byte[] STRANDS=new byte[] {'+', '-', '?', '.'};
+	public static final int PLUS=0, MINUS=1, QMARK=2, DOT=3;
+	public static final String DOTS=".";
+	
+	public static boolean parseSeqid=true;
+	public static boolean paseSource=false;
+	public static boolean parseType=true;
+	public static boolean parseScore=false;
+	public static boolean parseAttributes=true;
+	
+//	public static boolean parseSeqid=true;
+//	public static boolean paseSource=true;
+//	public static boolean parseType=true;
+//	public static boolean parseScore=true;
+//	public static boolean parseAttributes=true;
+	
+}