src/lib/nibTwo.c 1.6

Index: src/lib/nibTwo.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/lib/nibTwo.c,v
retrieving revision 1.5
retrieving revision 1.6
diff -b -B -U 1000000 -r1.5 -r1.6
--- src/lib/nibTwo.c	10 Mar 2006 17:43:37 -0000	1.5
+++ src/lib/nibTwo.c	23 Mar 2010 17:09:47 -0000	1.6
@@ -1,114 +1,123 @@
 /* nibTwo - Something to let you transparently access either
  * .2bit or .nib files. */
 
 #include "common.h"
 #include "hash.h"
 #include "dnaseq.h"
 #include "nib.h"
 #include "twoBit.h"
 #include "nibTwo.h"
 
 static char const rcsid[] = "$Id$";
 
 struct nibTwoCache *nibTwoCacheNew(char *pathName)
 /* Get something that will more or less transparently get sequence from 
  * nib files or .2bit. */ 
 {
 struct nibTwoCache *ntc;
 AllocVar(ntc);
 ntc->pathName = cloneString(pathName);
 ntc->isTwoBit = twoBitIsFile(pathName);
 if (ntc->isTwoBit)
     ntc->tbf = twoBitOpen(pathName);
 else
     ntc->nibHash = newHash(10);
 return ntc;
 }
 
 void nibTwoCacheFree(struct nibTwoCache **pNtc)
 /* Free up resources associated with nibTwoCache. */
 {
 struct nibTwoCache *ntc = *pNtc;
 if (ntc != NULL)
     {
     freez(&ntc->pathName);
     if (ntc->isTwoBit)
         twoBitClose(&ntc->tbf);
     else
         {
 	struct hashEl *el, *list = hashElListHash(ntc->nibHash);
 	struct nibInfo *nib;
 	for (el = list; el != NULL; el = el->next)
 	     {
 	     nib = el->val;
 	     nibInfoFree(&nib);
 	     }
 	hashElFreeList(&list);
 	hashFree(&ntc->nibHash);
 	}
     freez(pNtc);
     }
 }
 
 struct dnaSeq *nibTwoCacheSeq(struct nibTwoCache *ntc, char *seqName)
 /* Return all of sequence. This will have repeats in lower case. */
 {
 if (ntc->isTwoBit)
     return twoBitReadSeqFrag(ntc->tbf, seqName, 0, 0);
 else
     {
     struct nibInfo *nib = nibInfoFromCache(ntc->nibHash, ntc->pathName, seqName);
     return nibLdPart(nib->fileName, nib->f, nib->size, 0, nib->size);
     }
 }
 
 struct dnaSeq *nibTwoCacheSeqPartExt(struct nibTwoCache *ntc, char *seqName, int start, int size,
                                      boolean doMask, int *retFullSeqSize)
 /* Return part of sequence. If *retFullSeqSize is non-null then return full
  * size of sequence (not just loaded part) there.   Sequence will be lower
  * case if doMask is false, mixed case (repeats in lower)
  * if doMask is true. */
 {
 if (ntc->isTwoBit)
     {
     return twoBitReadSeqFragExt(ntc->tbf, seqName, start, start+size,
                                 doMask, retFullSeqSize);
     }
 else
     {
     struct nibInfo *nib = nibInfoFromCache(ntc->nibHash, ntc->pathName, seqName);
     int opts = (doMask ? NIB_MASK_MIXED : 0);
     if (retFullSeqSize != NULL)
         *retFullSeqSize = nib->size;
     return nibLdPartMasked(opts, nib->fileName, nib->f, nib->size, start, size);
     }
 }
 
 struct dnaSeq *nibTwoCacheSeqPart(struct nibTwoCache *ntc, char *seqName, int start, int size,
 	int *retFullSeqSize)
 /* Return part of sequence. If *retFullSeqSize is non-null then return full size of
  * sequence (not just loaded part) there. This will have repeats in lower case. */
 {
 return nibTwoCacheSeqPartExt(ntc, seqName, start, size, TRUE, retFullSeqSize);
 }
 
 struct dnaSeq *nibTwoLoadOne(char *pathName, char *seqName)
 /* Return sequence from a directory full of nibs or a .2bit file. 
  * The sequence will have repeats in lower case. */
 {
 struct dnaSeq *seq;
 if (twoBitIsFile(pathName))
     {
     struct twoBitFile *tbf = twoBitOpen(pathName);
     seq = twoBitReadSeqFrag(tbf, seqName, 0, 0);
     twoBitClose(&tbf);
     }
 else
     {
     char path[512];
     safef(path, sizeof(path), "%s/%s.nib", pathName, seqName);
     seq = nibLoadAllMasked(NIB_MASK_MIXED, path);
     }
 return seq;
 }
 
+int nibTwoGetSize(struct nibTwoCache *ntc, char *seqName)
+/* Return size of sequence. */
+{
+if (ntc->isTwoBit)
+    return twoBitSeqSize(ntc->tbf, seqName);
+else
+    return nibInfoFromCache(ntc->nibHash, ntc->pathName, seqName)->size;
+}
+