7e49f8f7b02b41d0bab2051250a3a08ce4ffafd0
braney
  Fri May 17 11:45:39 2024 -0700
ongoing work on pairBrowser

diff --git src/hg/utils/buildPairAssembly/buildPairAssembly.c src/hg/utils/buildPairAssembly/buildPairAssembly.c
index 9f6fc08..53e284e 100644
--- src/hg/utils/buildPairAssembly/buildPairAssembly.c
+++ src/hg/utils/buildPairAssembly/buildPairAssembly.c
@@ -2,31 +2,31 @@
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "chain.h"
 #include "twoBit.h"
 #include "dnaseq.h"
 #include "psl.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "buildPairAssembly - From a single coverage chain build a pairwise assembly including all sequence from both query and target\n"
   "usage:\n"
-  "   buildPairAssembly input.chain tSequenceName tSeq.2bit qSequenceName qSeq.2bit out.fa query.psl target.psl map.bed\n"
+  "   buildPairAssembly input.chain tSequenceName tSeq.2bit qSequenceName qSeq.2bit out.fa query.psl target.psl map.bed dup.bed mismatch.bed\n"
   "options:\n"
   "   -xxx=XXX\n"
   );
 }
 
 /* Command line validation table. */
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 struct linearBlock
 {
 struct linearBlock *next;
 unsigned tStart, tEnd;
 unsigned qStart, qEnd;
@@ -37,162 +37,245 @@
 /* Compare to sort based on target start. */
 {
 const struct linearBlock *a = *((struct linearBlock **)va);
 const struct linearBlock *b = *((struct linearBlock **)vb);
 return a->qStart - b->qStart;
 }
 
 int lbCmpTarget(const void *va, const void *vb)
 /* Compare to sort based on target start. */
 {
 const struct linearBlock *a = *((struct linearBlock **)va);
 const struct linearBlock *b = *((struct linearBlock **)vb);
 return a->tStart - b->tStart;
 }
 
-void buildPairAssembly(char *inputChain, char *tSequenceName, char *t2bitName, char *qSequenceName, char *q2bitName, char *outFaName, char *outQueryPsl, char *outTargetPsl, char *outMapBed)
+void outOverlap(FILE *f, char *tSequenceName,char *qSequenceName, struct cBlock *first,  struct cBlock *second, int count)
+{
+printf("first %d %d second %d %d\n", first->tStart, first->tEnd, second->tStart, second->tEnd);
+if (first->tEnd >= second->tEnd)
+    {
+    second->score = 3;
+    fprintf(f, "%s %d %d %s %d %d %d\n",qSequenceName, second->qStart, second->qEnd, tSequenceName, second->tStart, second->tEnd, count);
+    }
+else
+    errAbort("oops");
+
+/*
+first->tEnd = second->tStart;
+
+if (first->tStart == first->tEnd)
+    first->score = 3;
+first->qEnd  = second->qStart;
+*/
+
+}
+
+void buildPairAssembly(char *inputChain, char *tSequenceName, char *t2bitName, char *qSequenceName, char *q2bitName, char *outFaName, char *outQueryPsl, char *outTargetPsl, char *outMapBed, char *outDupBed, char *outMissBed)
 /* buildPairAssembly - From a single coverage chain build a pairwise assembly including all sequence from both query and target. */
 {
 struct lineFile *lf = lineFileOpen(inputChain, TRUE);
 struct chain *chain;
 struct cBlock *blockList = NULL, *cBlock, *nextBlock;
 struct twoBitFile *q2bit = twoBitOpen(q2bitName);
 struct twoBitFile *t2bit = twoBitOpen(t2bitName);
 FILE *outFa = mustOpen(outFaName, "w");
 FILE *outMap = mustOpen(outMapBed, "w");
+FILE *outDup = mustOpen(outDupBed, "w");
+FILE *outMiss = mustOpen(outMissBed, "w");
 
 fprintf(outFa, ">buildPair\n");
 
 while ((chain = chainRead(lf)) != NULL)
     {
     if (!sameString(tSequenceName, chain->tName) || !sameString(qSequenceName, chain->qName))
         continue;
 
     for (cBlock = chain->blockList; cBlock; cBlock = nextBlock)
         {
         nextBlock = cBlock->next;
         if (chain->qStrand == '-')
             {
             unsigned qStart = cBlock->qStart;
             cBlock->qStart = chain->qSize - cBlock->qEnd;
             cBlock->qEnd = chain->qSize - qStart;
             cBlock->score = 1;
             }
         else
             cBlock->score = 0;
 
         slAddHead(&blockList, cBlock);
         }
     }
 
+slSort(&blockList, cBlockCmpTarget);
+unsigned prevBase = blockList->tEnd;
+//unsigned prevBase = 0;
+boolean firstBlock = TRUE;
+struct cBlock *prevCBlock = NULL;
+int count = 0;
+
+for (cBlock = blockList->next; cBlock; cBlock = cBlock->next)
+    {
+    //if (cBlock->score == 2)
+        //continue;
+    if (!firstBlock)
+        {
+        if (cBlock->tStart < prevBase)
+            {
+            outOverlap(outDup, tSequenceName, qSequenceName, prevCBlock, cBlock, count++);
+            //printf("tBlock overlap %d %d\n", cBlock->tStart, prevBase);
+            //cBlock->score = 3;
+            continue;
+            }
+        }
+    else 
+        firstBlock = FALSE;
+    prevBase = cBlock->tEnd;
+    prevCBlock = cBlock;
+    }
+
 slSort(&blockList, cBlockCmpQuery);
-unsigned prevBase = blockList->qEnd;
+prevBase = blockList->qEnd;
 struct linearBlock *linearBlock;
 for (cBlock = blockList->next; cBlock;  cBlock = cBlock->next)
     {
+    if (cBlock->score == 3)
+        continue;
     if (cBlock->qStart < prevBase)
         {
         //printf("qBlock overlap %d %d\n", cBlock->qStart, prevBase);
         cBlock->score = 2;
         continue;
         }
     if (cBlock->qStart > prevBase)
         {
         AllocVar(linearBlock);
         linearBlock->qStart = prevBase;
         linearBlock->qEnd = cBlock->qStart;
         if (cBlock->score == 1)
             linearBlock->isFlipped = TRUE;
         cBlock->data = (void *)linearBlock;
         }
     prevBase = cBlock->qEnd;
     }
 
 slSort(&blockList, cBlockCmpTarget);
+//prevBase = blockList->tEnd;
 prevBase = 0;
 struct linearBlock *linearBlockList = NULL;
-boolean firstBlock = TRUE;
+firstBlock = TRUE;
+prevCBlock = NULL;
 
 for (cBlock = blockList; cBlock;   cBlock = cBlock->next)
     {
-    if (cBlock->tStart < prevBase)
-        {
-        //printf("tBlock overlap %d %d\n", cBlock->tStart, prevBase);
-        continue;
-        }
-    if (cBlock->score == 2)
+    if (cBlock->score >= 2)
         continue;
     if (!firstBlock)
         {
         if (cBlock->tStart > prevBase)
             {
             AllocVar(linearBlock);
             linearBlock->tStart = prevBase;
             linearBlock->tEnd = cBlock->tStart;
             slAddHead(&linearBlockList, linearBlock);
             }
+
         if (cBlock->data != NULL)
             {
             struct linearBlock *qInsert = (struct linearBlock *)cBlock->data;
             slAddHead(&linearBlockList, qInsert);
             }
         }
     else 
         firstBlock = FALSE;
 
     AllocVar(linearBlock);
     linearBlock->qStart = cBlock->qStart;
     linearBlock->qEnd = cBlock->qEnd;
     linearBlock->tStart = cBlock->tStart;
     linearBlock->tEnd = cBlock->tEnd;
     if (cBlock->score == 1)
         linearBlock->isFlipped = TRUE;
     slAddHead(&linearBlockList, linearBlock);
 
     prevBase = cBlock->tEnd;
+    prevCBlock = cBlock;
     }
 
 slReverse(&linearBlockList);
 
+#define BOTH_COLOR       "20,40,140"
+#define INVERT_COLOR       "140,20,140"
+#define REFONLY_COLOR       "255,255,0"
+#define QUERYONLY_COLOR       "170,255,60"
+
 unsigned startAddress = 0, size;
+boolean firstBlockFlipped = linearBlockList->isFlipped;
+char strand;
+char *color;
 for(linearBlock = linearBlockList; linearBlock; linearBlock = linearBlock->next)
     {
+ //   printf("start %d %d\n", linearBlock->tStart, linearBlock->tEnd);
     if (linearBlock->qStart == linearBlock->qEnd)
         {
         struct dnaSeq *dna = twoBitReadSeqFrag(t2bit, tSequenceName, linearBlock->tStart, linearBlock->tEnd);
         fprintf(outFa, "%s\n", (char *)dna->dna);
         size = linearBlock->tEnd - linearBlock->tStart;
         //printf("chr1 %d %d refOnly 0 + %d %d 255,255,0\n", startAddress, startAddress + size, linearBlock->isFlipped, linearBlock->tStart, linearBlock->tEnd);
-        fprintf(outMap,"buildPair %d %d refOnly 0 + %d %d 255,255,0\n", startAddress, startAddress + size, startAddress, startAddress + size);
+        //fprintf(outMap,"buildPair %d %d refOnly 0 + %d %d 255,255,0\n", startAddress, startAddress + size, startAddress, startAddress + size);
+        fprintf(outMap,"buildPair %d %d refOnly 0 + %d %d %s %d %d 0 0\n", startAddress, startAddress + size,  startAddress, startAddress + size, REFONLY_COLOR, linearBlock->tStart, linearBlock->tEnd);
         }
     else if (linearBlock->tStart == linearBlock->tEnd)
         {
         struct dnaSeq *dna = twoBitReadSeqFrag(q2bit, qSequenceName, linearBlock->qStart, linearBlock->qEnd);
         fprintf(outFa, "%s\n", (char *)dna->dna);
         size = linearBlock->qEnd - linearBlock->qStart;
         char strand = linearBlock->isFlipped ? '-' : '+';
         //printf("chr1 %d %d %d queryOnly %d %d\n", startAddress, startAddress + size, linearBlock->isFlipped, linearBlock->qStart, linearBlock->qEnd);
-        fprintf(outMap,"buildPair %d %d queryOnly 0 %c %d %d 170,255,60\n", startAddress, startAddress + size, strand, startAddress, startAddress + size);
+        //fprintf(outMap,"buildPair %d %d queryOnly 0 %c %d %d 170,255,60\n", startAddress, startAddress + size, strand, startAddress, startAddress + size);
+        fprintf(outMap,"buildPair %d %d queryOnly 0 %c %d %d %s 0 0 %d %d\n", startAddress, startAddress + size, strand, startAddress, startAddress + size, QUERYONLY_COLOR, linearBlock->qStart, linearBlock->qEnd);
         }
     else
         {
         struct dnaSeq *dna = twoBitReadSeqFrag(t2bit, tSequenceName, linearBlock->tStart, linearBlock->tEnd);
         fprintf(outFa, "%s\n", (char *)dna->dna);
+        struct dnaSeq *dna2 = twoBitReadSeqFrag(q2bit, qSequenceName, linearBlock->qStart, linearBlock->qEnd);
         size = linearBlock->qEnd - linearBlock->qStart;
-        char strand = linearBlock->isFlipped ? '-' : '+';
+        if (linearBlock->isFlipped)
+            reverseComplement(dna2->dna, size);
+        int ii;
+        for(ii = 0; ii < size; ii++)
+            {
+            if (toupper(dna->dna[ii]) != toupper(dna2->dna[ii]))
+                fprintf(outMiss, "buildPair %d %d %c->%c\n", startAddress + ii, startAddress + ii + 1, toupper(dna->dna[ii]), toupper(dna2->dna[ii]));
+
+            }
+        if (linearBlock->isFlipped == firstBlockFlipped)
+            {
+            strand = '+';
+            color = BOTH_COLOR;
+            }
+        else
+            {
+            strand = '-';
+            color = INVERT_COLOR;
+            }
+        //char strand = linearBlock->isFlipped ? '-' : '+';
         //printf("chr1 %d %d both 0 %c  %d %d %d %d\n", startAddress, startAddress + size, linearBlock->isFlipped,linearBlock->tStart, linearBlock->tEnd, linearBlock->qStart, linearBlock->qEnd);
-        fprintf(outMap,"buildPair %d %d both 0 %c  %d %d 20,40,140\n", startAddress, startAddress + size, strand,  startAddress, startAddress + size); 
+        //fprintf(outMap,"buildPair %d %d both 0 %c  %d %d 20,40,140\n", startAddress, startAddress + size, strand,  startAddress, startAddress + size); 
+        fprintf(outMap,"buildPair %d %d both 0 %c %d %d %s %d %d %d %d\n", startAddress, startAddress + size, strand, startAddress, startAddress + size, color, linearBlock->tStart, linearBlock->tEnd, linearBlock->qStart, linearBlock->qEnd);
         }
     startAddress += size;
     }
 
 unsigned sumSize = startAddress;
 unsigned tSize = twoBitSeqSize(t2bit, tSequenceName);
 unsigned qSize = twoBitSeqSize(q2bit, qSequenceName);
 printf("qSize %d\n", qSize);
 FILE *outQuery = mustOpen(outQueryPsl, "w");
 FILE *outTarget = mustOpen(outTargetPsl, "w");
 startAddress = 0;
 for(linearBlock = linearBlockList; linearBlock; linearBlock = linearBlock->next)
     {
     if (linearBlock->qStart == linearBlock->qEnd)
         {
@@ -276,20 +359,20 @@
         {
         if (linearBlock->qStart != startAddress)
             errAbort("qStart %d %d", startAddress, linearBlock->qStart);
         }
     else
         firstBlock = FALSE;
     startAddress = linearBlock->qEnd;
     }
 
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
-if (argc != 10)
+if (argc != 12)
     usage();
-buildPairAssembly(argv[1], argv[2], argv[3], argv[4], argv[5], argv[6], argv[7], argv[8], argv[9]);
+buildPairAssembly(argv[1], argv[2], argv[3], argv[4], argv[5], argv[6], argv[7], argv[8], argv[9], argv[10], argv[11]);
 return 0;
 }