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package tracker;
import shared.Tools;
import structures.ByteBuilder;
import structures.Crispr;
import structures.LongList;
import structures.Range;
/**
* Tracks crispr stats.
*
* @author Brian Bushnell
* @date Sept 5, 2023
*
*/
public class CrisprTracker {
/*--------------------------------------------------------------*/
/*---------------- Initialization ----------------*/
/*--------------------------------------------------------------*/
public void add(final Crispr p, final byte[] s) {
Range r=(p.b.length()>p.a.length() ? p.b : p.a);
int sstart=p.a.b+1, sstop=p.b.a-1;
float rgc=Tools.calcGC(s, r.a, r.b);
float sgc=Tools.calcGC(s, sstart, sstop);
int rgci=(int)(Math.round(rgc*gcMult));
int sgci=(int)(Math.round(sgc*gcMult));
int rlen=r.length();
int slen=sstop-sstart+1;
int ulen=rlen+slen;
int tlen=p.b.b-p.a.a+1;
rlenList.increment(rlen);
slenList.increment(slen);
ulenList.increment(ulen);
tlenList.increment(tlen);
rgcList.increment(rgci);
sgcList.increment(sgci);
matchList.increment(p.matches);
mismatchList.increment(p.mismatches);
crisprsFound++;
// partialTipRepeats+=((p.a.length()==p.b.length()) ? 0 : 1);
partialTipRepeats+=((p.a.length()==p.b.length() && p.a.a>0 && p.b.b<s.length-1) ? 0 : 1);
//Matches, mismatches, and copies need to be incremented manually
}
/*--------------------------------------------------------------*/
/*---------------- Methods ----------------*/
/*--------------------------------------------------------------*/
public CrisprTracker add(CrisprTracker p) {
for(int i=0; i<lists.length; i++) {
lists[i].incrementBy(p.lists[i]);
}
crisprsFound+=p.crisprsFound;
readsWithCrisprs+=p.readsWithCrisprs;
trimmedByConsensus+=p.trimmedByConsensus;
partialTipRepeats+=p.partialTipRepeats;
modifiedByRef+=p.modifiedByRef;
alignedToRef+=p.alignedToRef;
failedAlignment+=p.failedAlignment;
alignments+=p.alignments;
alignmentRequested+=p.alignmentRequested;
return this;
}
public ByteBuilder appendTo(ByteBuilder bb) {
return PalindromeTracker.append(bb,
"#Value\trepeat\tspacer\tperiod\ttotal\trGC\tsGC\tmatch\tmismtch\tcopies\trefmm\trefmmv",
lists, histmax);
}
@Override
public String toString() {
return appendTo(new ByteBuilder()).toString();
}
/*--------------------------------------------------------------*/
/*---------------- Fields ----------------*/
/*--------------------------------------------------------------*/
private final int[] acgtn=new int[5];
public long crisprsFound=0;
public long readsWithCrisprs=0;
public long trimmedByConsensus=0;
public long partialTipRepeats=0;
public long alignedToRef=0;
public long modifiedByRef=0;
public long failedAlignment=0;
public long alignments=0;
public long alignmentRequested=0;
/** Repeat length */
public LongList rlenList=new LongList();
/** Spacer length */
public LongList slenList=new LongList();
/** Length of a spacer+repeat */
public LongList ulenList=new LongList();
/** Total length */
public LongList tlenList=new LongList();
/** Number of matches */
public LongList matchList=new LongList();
/** Number of mismatches between repeats */
public LongList mismatchList=new LongList();
/** Copy count of this repeat */
public LongList copyList=new LongList();
/** Repeat gc, in 2% increments */
public LongList rgcList=new LongList(51);
/** Spacer gc, in 2% increments */
public LongList sgcList=new LongList(51);
/** Number of mismatches with reference */
public LongList refMismatchList=new LongList(51);
/** Number of mismatches with reference for valid alignments */
public LongList refMismatchListValid=new LongList(51);
public final LongList[] lists={rlenList, slenList, ulenList, tlenList,
rgcList, sgcList, matchList, mismatchList,
copyList, refMismatchList, refMismatchListValid};
/*--------------------------------------------------------------*/
/*---------------- Statics ----------------*/
/*--------------------------------------------------------------*/
public static int histmax=150;
public static int gcMult=100;
}
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