c442d3afa2063b13c887983131439855665a79a0
kent
  Wed Feb 27 10:39:02 2013 -0800
Moving general purpose routines from bigBedNamedItems to appropriate library.
diff --git src/utils/bigBedNamedItems/bigBedNamedItems.c src/utils/bigBedNamedItems/bigBedNamedItems.c
index 09c8c70..9f354d7 100644
--- src/utils/bigBedNamedItems/bigBedNamedItems.c
+++ src/utils/bigBedNamedItems/bigBedNamedItems.c
@@ -1,198 +1,47 @@
 /* bigBedNamedItems - Extract item(s) of given name(s) from bigBed. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "localmem.h"
 #include "udc.h"
 #include "bPlusTree.h"
 #include "bigBed.h"
 #include "obscure.h"
 #include "zlibFace.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "bigBedNamedItems - Extract item of given name from bigBed\n"
   "usage:\n"
   "   bigBedNamedItems file.bb name output.bed\n"
-  "options:\n"
-  "   -xxx=XXX\n"
   );
 }
 
 /* Command line validation table. */
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
-void bigBedAttachNameIndex(struct bbiFile *bbi)
-/* Attach name index part of bbiFile to bbi */
-{
-if (bbi->nameBpt == NULL)
-    {
-    if (bbi->nameIndexOffset == 0)
-	errAbort("%s has no name index", bbi->fileName);
-    udcSeek(bbi->udc, bbi->nameIndexOffset);
-    bbi->nameBpt = bptFileAttach(bbi->fileName, bbi->udc);
-    }
-}
-
-struct offsetSize 
-/* Simple file offset and file size. */
-    {
-    bits64 offset; 
-    bits64 size;
-    };
-
-int cmpOffsetSizeRef(const void *va, const void *vb)
-/* Compare to sort slRef pointing to offsetSize.  Sort is kind of hokey,
- * but guarantees all items that are the same will be next to each other
- * at least, which is all we care about. */
-{
-const struct slRef *a = *((struct slRef **)va);
-const struct slRef *b = *((struct slRef **)vb);
-return memcmp(a->val, b->val, sizeof(struct offsetSize));
-}
-
-struct fileOffsetSize *bigBedChunksMatchingName(struct bbiFile *bbi, char *name)
-/* Get list of file chunks that match name.  Can slFreeList this when done. */
-{
-bigBedAttachNameIndex(bbi);
-struct slRef *blockList = bptFileFindMultiple(bbi->nameBpt, name, strlen(name), sizeof(struct offsetSize));
-slSort(&blockList, cmpOffsetSizeRef);
-
-struct fileOffsetSize *fosList = NULL, *fos;
-struct offsetSize lastOffsetSize = {0,0};
-struct slRef *blockRef;
-for (blockRef = blockList; blockRef != NULL; blockRef = blockRef->next)
-    {
-    if (memcmp(&lastOffsetSize, blockRef->val, sizeof(lastOffsetSize)) != 0)
-        {
-	memcpy(&lastOffsetSize, blockRef->val, sizeof(lastOffsetSize));
-	AllocVar(fos);
-	if (bbi->isSwapped)
-	    {
-	    fos->offset = byteSwap64(lastOffsetSize.offset);
-	    fos->size = byteSwap64(lastOffsetSize.size);
-	    }
-	else
-	    {
-	    fos->offset = lastOffsetSize.offset;
-	    fos->size = lastOffsetSize.size;
-	    }
-	slAddHead(&fosList, fos);
-	}
-    }
-slRefFreeListAndVals(&blockList);
-slReverse(&fosList);
-return fosList;
-}
-
-struct bigBedInterval *bigBedNameQuery(struct bbiFile *bbi, char *name, struct lm *lm)
-/* Return list of intervals matching file. These intervals will be allocated out of lm. */
-{
-bigBedAttachNameIndex(bbi);
-boolean isSwapped = bbi->isSwapped;
-struct fileOffsetSize *fos, *fosList = bigBedChunksMatchingName(bbi, name);
-struct bigBedInterval *interval, *intervalList = NULL;
-for (fos = fosList; fos != NULL; fos = fos->next)
-    {
-    /* Read in raw data */
-    udcSeek(bbi->udc, fos->offset);
-    char *rawData = needLargeMem(fos->size);
-    udcRead(bbi->udc, rawData, fos->size);
-
-    /* Optionally uncompress data, and set data pointer to uncompressed version. */
-    char *uncompressedData = NULL;
-    char *data = NULL;
-    int dataSize = 0;
-    if (bbi->uncompressBufSize > 0)
-	{
-	data = uncompressedData = needLargeMem(bbi->uncompressBufSize);
-	dataSize = zUncompress(rawData, fos->size, uncompressedData, bbi->uncompressBufSize);
-	}
-    else
-	{
-        data = rawData;
-	dataSize = fos->size;
-	}
-
-    /* Set up for "memRead" routines to more or less treat memory block like file */
-    char *blockPt = data, *blockEnd = data + dataSize;
-    struct dyString *dy = dyStringNew(32); // Keep bits outside of chrom/start/end here
-
-
-    /* Read next record into local variables. */
-    while (blockPt < blockEnd)
-	{
-	bits32 chromIx = memReadBits32(&blockPt, isSwapped);
-	bits32 s = memReadBits32(&blockPt, isSwapped);
-	bits32 e = memReadBits32(&blockPt, isSwapped);
-	int c;
-	dyStringClear(dy);
-	while ((c = *blockPt++) >= 0)
-	    {
-	    if (c == 0)
-		break;
-	    dyStringAppendC(dy, c);
-	    }
-	if (startsWithWordByDelimiter(name, '\t', dy->string))
-	    {
-	    lmAllocVar(lm, interval);
-	    interval->start = s;
-	    interval->end = e;
-	    interval->rest = cloneString(dy->string);
-	    interval->chromId = chromIx;
-	    slAddHead(&intervalList, interval);
-	    }
-	}
-
-    /* Clean up temporary buffers. */
-    dyStringFree(&dy);
-    freez(&uncompressedData);
-    freez(&rawData);
-    }
-slFreeList(&fosList);
-slReverse(&intervalList);
-return intervalList;
-}
-
-void bigBedIntervalListToBedFile(struct bbiFile *bbi, struct bigBedInterval *intervalList, FILE *f)
-/* Write out big bed interval list to bed file,  looking up chromosome mostly */
-{
-char chromName[bbi->chromBpt->keySize+1];
-int chromId = -1;
-struct bigBedInterval *interval;
-for (interval = intervalList; interval != NULL; interval = interval->next)
-    {
-    if (interval->chromId != chromId)
-        {
-	chromId = interval->chromId;
-	bptStringKeyAtPos(bbi->chromBpt, chromId, chromName, sizeof(chromName));
-	}
-    fprintf(f, "%s\t%u\t%u\t%s\n", chromName, interval->start, interval->end, interval->rest);
-    }
-}
-
 void bigBedNamedItems(char *bigBedFile, char *name, char *outFile)
 /* bigBedNamedItems - Extract item(s) of given name(s) from bigBed. */
 {
 struct bbiFile *bbi = bigBedFileOpen(bigBedFile);
 FILE *f = mustOpen(outFile, "w");
 struct lm *lm = lmInit(0);
 struct bigBedInterval *intervalList = bigBedNameQuery(bbi, name, lm);
 bigBedIntervalListToBedFile(bbi, intervalList, f);
 carefulClose(&f);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 4)
     usage();
 bigBedNamedItems(argv[1], argv[2], argv[3]);
 return 0;
 }