533112afe2a2005e80cdb1f82904ea65032d4302
braney
  Sat Oct 2 11:37:34 2021 -0700
split hg/lib into two separate libaries, one only used by the cgis

diff --git src/hg/lib/axtLib.c src/hg/lib/axtLib.c
deleted file mode 100644
index 1cd5fff..0000000
--- src/hg/lib/axtLib.c
+++ /dev/null
@@ -1,192 +0,0 @@
-/* axtLib - Convert chain to axt */
-
-/* Copyright (C) 2014 The Regents of the University of California 
- * See README in this or parent directory for licensing information. */
-#include "common.h"
-#include "linefile.h"
-#include "hash.h"
-#include "options.h"
-#include "chainBlock.h"
-#include "dnautil.h"
-#include "dnaseq.h"
-#include "chainNet.h"
-#include "nib.h"
-#include "axt.h"
-#include "axtLib.h"
-#include "axtInfo.h"
-#include "chainToAxt.h"
-#include "hdb.h"
-
-
-
-struct axt *netFillToAxt(struct cnFill *fill, struct dnaSeq *tChrom , int tSize,
-	struct hash *qChromHash, char *nibDir,
-	struct chain *chain, boolean swap)
-/* Convert subset of chain as defined by fill to axt. swap query and target if swap is true*/
-{
-struct dnaSeq *qSeq;
-boolean isRev = (chain->qStrand == '-');
-struct chain *subChain, *chainToFree;
-int qOffset;
-struct axt *axtList = NULL , *axt;
-struct nibInfo *nib = hashFindVal(qChromHash, fill->qName);
-
-/* Get query sequence fragment. */
-    {
-    if (nib == NULL)
-        {
-	char path[512];
-	AllocVar(nib);
-	safef(path, sizeof(path), "%s/%s.nib", nibDir, fill->qName);
-	nib->fileName = cloneString(path);
-	nibOpenVerify(path, &nib->f, &nib->size);
-	hashAdd(qChromHash, fill->qName, nib);
-	}
-    qSeq = nibLoadPartMasked(NIB_MASK_MIXED, nib->fileName, 
-    	fill->qStart, fill->qSize);
-    if (isRev)
-	{
-        reverseComplement(qSeq->dna, qSeq->size);
-	qOffset = nib->size - (fill->qStart + fill->qSize);
-	}
-    else
-	qOffset = fill->qStart;
-    }
-chainSubsetOnT(chain, fill->tStart, fill->tStart + fill->tSize, 
-	&subChain, &chainToFree);
-if (subChain != NULL)
-    {
-    axtList = chainToAxt(subChain, qSeq, qOffset, tChrom, fill->tStart, 100, BIGNUM);
-    if (swap)
-        {
-        for (axt = axtList ; axt != NULL ; axt = axt->next)
-            axtSwap(axt, tSize, nib->size);
-        }
-    }
-chainFree(&chainToFree);
-freeDnaSeq(&qSeq);
-return axtList;
-}
-
-void axtListReverse(struct axt **axtList, char *queryDb)
-/* reverse complement an entire axtList */
-{
-struct axt *axt;
-int tmp;
-
-for (axt = *axtList; axt != NULL; axt = axt->next)
-    {
-    int qSize = 0;
-        
-    if (sameString(axt->qName , "gap"))
-        qSize = axt->qEnd;
-    else
-        qSize = hChromSize(queryDb, axt->qName);
-
-    reverseComplement(axt->qSym, axt->symCount);
-    reverseComplement(axt->tSym, axt->symCount);
-    tmp = qSize - axt->qStart;
-    axt->qStart = qSize - axt->qEnd;
-    axt->qEnd = tmp;
-    }
-slReverse(axtList);
-}
-
-struct axt *createAxtGap(char *nibFile, char *chrom, 	
-			 int start, int end, char strand)
-/* return an axt alignment with the query all deletes - null aligment */
-{
-struct axt *axt;
-int size = end-start;
-char *gapPt = needLargeMem(size+1);
-char *p;
-struct dnaSeq *seq = NULL;
-
-for (p=gapPt;p<=gapPt+size;p++)
-    *p = '-';
-AllocVar(axt);
-axt->tName = chrom;
-axt->tStart = start;
-axt->tEnd = end;
-axt->tStrand = strand;
-axt->qName = "gap";
-axt->qStart = 1;
-axt->qEnd = size;
-axt->qStrand = strand;
-axt->symCount = size;
-axt->score = 0;
-seq = nibLoadPart(nibFile, start,size);
-axt->tSym = cloneMem(seq->dna, size+1);
-axt->qSym = cloneMem(gapPt, size+1);
-return axt;
-}
-
-void axtFillGap(struct axt **aList, char *nibDir, char direction)
-/* fill gaps between blocks with null axts with seq on t and q seq all gaps*/
-/* direction = '+' ascending on + strand, - is descending on - strand */
-{
-struct axt *axt, *next, *axtGap, *tmp, *prevAxt = NULL;
-int prevEnd = 0;
-int prevStart = 0;
-char nib[128];
-
-for (axt = *aList; axt != NULL; axt = next)
-    {
-    if (((axt->tStart)-1) > prevEnd  && prevEnd > 0 && direction == '+')
-        {
-        assert(prevAxt != NULL);
-        tmp = prevAxt->next;
-        safef(nib, sizeof(nib), "%s/%s.nib",nibDir,axt->tName);
-        axtGap = createAxtGap(nib,axt->tName,prevEnd,(axt->tStart),axt->qStrand);
-        axtGap->next = tmp;
-        prevAxt->next = axtGap;
-        }
-    if (((axt->tEnd)+1) < prevStart  && prevStart > 0 && direction == '-')
-        {
-        assert(prevAxt != NULL);
-        tmp = prevAxt->next;
-        safef(nib, sizeof(nib), "%s/%s.nib",nibDir,axt->tName);
-        axtGap = createAxtGap(nib,axt->tName,(axt->tEnd),prevStart,axt->qStrand);
-        axtGap->next = tmp;
-        prevAxt->next = axtGap;
-        }
-    prevEnd = axt->tEnd;
-    prevStart = axt->tStart;
-    prevAxt = axt;
-    next = axt->next;
-    }
-}
-char *getAxtFileName(char *chrom, char *toDb, char *alignment, char *fromDb)
-/* return file name for a axt alignment */
-{
-char query[256];
-struct sqlResult *sr;
-struct sqlConnection *conn = hAllocConn(fromDb);
-char **row;
-struct axtInfo *ai = NULL;
-
-if (alignment != NULL)
-    sqlSafef(query, sizeof(query),
-	     "select * from axtInfo where chrom = '%s' and species = '%s' and alignment = '%s'",
-	     chrom, toDb, alignment);
-else
-    sqlSafef(query, sizeof(query),
-	     "select * from axtInfo where chrom = '%s' and species = '%s'",
-	     chrom, toDb);
-sr = sqlGetResult(conn, query);
-if ((row = sqlNextRow(sr)) != NULL)
-    {
-    ai = axtInfoLoad(row );
-    }
-if (ai == NULL)
-    {
-    printf("\nNo alignments available for %s (database %s).\n\n",
-	   hFreezeFromDb(toDb), toDb);
-    axtInfoFree(&ai);
-    return NULL;
-    }
-//axtInfoFree(&ai);
-return cloneString(ai->fileName);
-}
-
-