6e5ee11ca95cd971984038cf65bae00d9c898707
galt
  Wed Jun 4 15:40:02 2014 -0700
Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
diff --git src/jkOwnLib/gfInternal.c src/jkOwnLib/gfInternal.c
index 7c6ae82..f8fbd68 100644
--- src/jkOwnLib/gfInternal.c
+++ src/jkOwnLib/gfInternal.c
@@ -1,144 +1,144 @@
 /* Some stuff shared by gfClient and gfPcr. 
  * Copyright 2001-2004 Jim Kent. All rights reserved. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dnaseq.h"
 #include "genoFind.h"
 #include "gfInternal.h"
-#include "errabort.h"
+#include "errAbort.h"
 #include "nib.h"
 #include "twoBit.h"
 
 
 
 static int extendRespect(int oldX, int newX)
 /* Return newX modified slightly so as to be in same frame as oldX. */
 {
 int frame = oldX % 3;
 newX = newX - (newX % 3) + frame;
 return newX;
 }
 
 void gfiExpandRange(struct gfRange *range, int qSize, int tSize, 
 	boolean respectFrame, boolean isRc, int expansion)
 /* Expand range to cover an additional 500 bases on either side. */
 {
 int x;
 
 x = range->qStart - expansion;
 if (x < 0) x = 0;
 range->qStart = x;
 
 x = range->qEnd + expansion;
 if (x > qSize) x = qSize;
 range->qEnd = x;
 
 x = range->tStart - expansion;
 if (x < 0) x = 0;
 if (respectFrame && !isRc) 
     {
     x = extendRespect(range->tStart, x);
     }
 range->tStart = x;
 
 x = range->tEnd + expansion;
 if (x > tSize) x = tSize;
 if (respectFrame && isRc)
     {
     x = extendRespect(range->tEnd, x);
     if (x > tSize)
         x -= 3;
     }
 range->tEnd = x;
 }
 
 struct dnaSeq *gfiExpandAndLoadCached(struct gfRange *range, 
 	struct hash *tFileCache, char *tSeqDir, int querySize, 
 	int *retTotalSeqSize, boolean respectFrame, boolean isRc, int expansion)
 /* Expand range to cover an additional expansion bases on either side.
  * Load up target sequence and return. (Done together because don't
  * know target size before loading.) */
 {
 struct dnaSeq *target = NULL;
 char fileName[PATH_LEN+256];
 
 safef(fileName, sizeof(fileName), "%s/%s", tSeqDir, range->tName);
 if (nibIsFile(fileName))
     {
     struct nibInfo *nib = hashFindVal(tFileCache, fileName);
     if (nib == NULL)
         {
 	nib = nibInfoNew(fileName);
 	hashAdd(tFileCache, fileName, nib);
 	}
     if (isRc)
 	reverseIntRange(&range->tStart, &range->tEnd, nib->size);
     gfiExpandRange(range, querySize, nib->size, respectFrame, isRc, expansion);
     target = nibLdPart(fileName, nib->f, nib->size, 
     	range->tStart, range->tEnd - range->tStart);
     if (isRc)
 	{
 	reverseComplement(target->dna, target->size);
 	reverseIntRange(&range->tStart, &range->tEnd, nib->size);
 	}
     *retTotalSeqSize = nib->size;
     }
 else
     {
     struct twoBitFile *tbf = NULL;
     // split a filename+chrom like "/gbdb/hg19/hg19.2bit:chr1"
     // (can also be URL like "http://hgdownload.cse.ucsc.edu/gbdb/hg19/hg19.2bit:chr1")
     // into filename and tSeqName
     char *tSeqName = strrchr(fileName, ':');
     int tSeqSize = 0;
     if (tSeqName == NULL)
         errAbort("No colon in .2bit response from gfServer");
     *tSeqName++ = 0;
     tbf = hashFindVal(tFileCache, fileName);
     if (tbf == NULL)
         {
 	tbf = twoBitOpen(fileName);
 	hashAdd(tFileCache, fileName, tbf);
 	}
     tSeqSize = twoBitSeqSize(tbf, tSeqName);
     if (isRc)
 	reverseIntRange(&range->tStart, &range->tEnd, tSeqSize);
     gfiExpandRange(range, querySize, tSeqSize, respectFrame, isRc, expansion);
     target = twoBitReadSeqFragLower(tbf, tSeqName, range->tStart, range->tEnd);
     if (isRc)
 	{
 	reverseComplement(target->dna, target->size);
 	reverseIntRange(&range->tStart, &range->tEnd, tSeqSize);
 	}
     *retTotalSeqSize = tSeqSize;
     }
 return target;
 }
 
 void gfiGetSeqName(char *spec, char *name, char *file)
 /* Extract sequence name and optionally file name from spec, 
  * which includes nib and 2bit files.  (The file may be NULL
  * if you don't care.) */
 {
 if (nibIsFile(spec))
     {
     splitPath(spec, NULL, name, NULL);
     if (file != NULL)
         strcpy(file, spec);
     }
 else
     {
     char *s = strchr(spec, ':');
     if (s == NULL)
 	errAbort("Expecting colon in %s", spec);
     strcpy(name, s+1);
     if (file != NULL)
         {
 	int fileNameSize = s - spec;
 	memcpy(file, spec, fileNameSize);
 	file[fileNameSize] = 0;
 	}
     }
 }