0d573301aec0beac41da09b0152c5e74fbe7f2f2
markd
  Sun Dec 8 10:16:19 2024 -0800
Add generate name to output partation BEDs.  Remove -partSize, which made no sense to just group by number of partations.  It is replaced by -partMergeSize, to allow for merging partations within a certain distance

diff --git src/hg/utils/bedPartition/bedPartition.c src/hg/utils/bedPartition/bedPartition.c
index 3350843..b2f71ce 100644
--- src/hg/utils/bedPartition/bedPartition.c
+++ src/hg/utils/bedPartition/bedPartition.c
@@ -1,174 +1,177 @@
 /* bedPartition - split BED ranges into non-overlapping ranges  */
 
 /* Copyright (C) 2019 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 #include "common.h"
 #include "options.h"
 #include "partitionSort.h"
 #include "basicBed.h"
 #include "sqlNum.h"
 #include "dystring.h"
 #include "portable.h"
 
 
 /* command line options and values */
 static struct optionSpec optionSpecs[] =
 {
-    {"partSize", OPTION_INT},
+    {"partMergeSize", OPTION_INT},
     {"parallel", OPTION_INT},
     {NULL, 0}
 };
-static int gPartSize = 1;
+static int gPartMergeSize = 0;
 static int gParallel = 0;
 
 static void usage()
 /* Explain usage and exit. */
 {
 errAbort("bedPartition - split BED ranges into non-overlapping ranges\n"
   "usage:\n"
   "   bedPartition [options] bedFile rangesBed\n"
   "\n"
   "Split ranges in a BED into non-overlapping sets for use in cluster jobs.\n"
-  "Output is a BED 3 of the ranges.\n"
+  "Output is a BED 4 of the ranges and a generated name.\n"
   "The bedFile maybe compressed and no ordering is assumed.\n"
   "\n"
   "options:\n"
-  "   -partSize=1 - will combine non-overlapping partitions, up to\n"
-  "    this number of ranges.\n"
+  "   -partMergeSize=0 - will combine adjacent non-overlapping partitions, that are\n"
+  "    separated by no more that this number of bases.\n"
   "    per set of overlapping records.\n"
-  "   -parallel=n - use this many cores for parallel sorting\n");
+  "   -parallel=n - use this many cores for parallel sorting\n"
+  "notes:\n"
+  "   - Generate name is useful for testing if two ranges are in the same partition\n");
 }
 
 struct bedInput
 /* object to read a bed */
 {
     struct pipeline *pl;     /* sorting pipeline */
     struct lineFile *lf;     /* lineFile to pipeline */
     struct bed3 *pending;     /* next bed to read, if not NULL */
 };
 
 static struct bedInput *bedInputNew(char *bedFile)
 /* create object to read BEDs */
 {
 struct bedInput *bi;
 AllocVar(bi);
 bi->pl = partitionSortOpenPipeline(bedFile, 0, 1, 2, gParallel);
 bi->lf = pipelineLineFile(bi->pl);
 
 return bi;
 }
 
 static void bedInputFree(struct bedInput **biPtr)
 /* free bedInput object */
 {
 struct bedInput *bi = *biPtr;
 if (bi != NULL)
     {
     assert(bi->pending == NULL);
     pipelineClose(&bi->pl);
     freez(biPtr);
     }
 }
 
 static struct bed3 *bed3Next(struct lineFile *lf)
 /* read a BED3 */
 {
 char *row[3];
 if (!lineFileRow(lf, row))
     return NULL;
-return bed3New(row[0], sqlUnsigned(row[1]), sqlUnsigned(row[2]));
+// adjust start to allow for merge padding
+unsigned start = sqlUnsigned(row[1]);
+if (start > gPartMergeSize)  // don't underflow
+    start -= gPartMergeSize;
+return bed3New(row[0], start, sqlUnsigned(row[2]));
 }
 
 
 static struct bed3 *bedInputNext(struct bedInput *bi)
 /* read next bed */
 {
 struct bed3 *bed = bi->pending;
 if (bed != NULL)
     bi->pending = NULL;
 else
     bed = bed3Next(bi->lf);
 return bed;
 }
 
 static void bedInputPutBack(struct bedInput *bi, struct bed3 *bed)
 /* save bed pending slot. */
 {
 if (bi->pending)
     errAbort("only one bed maybe pending");
 bi->pending = bed;
 }
 
 static boolean sameChrom(struct bed3 *bed, struct bed3 *bedPart)
 /* chrom the same? */
 {
 return sameString(bed->chrom, bedPart->chrom);
 }
 
 static boolean isOverlapped(struct bed3 *bed, struct bed3 *bedPart)
 /* determine if a bed is in the partition */
 {
 return (bed->chromStart < bedPart->chromEnd) && (bed->chromEnd > bedPart->chromStart)
     && sameChrom(bed, bedPart);
 }
 
 
 static struct bed3 *readPartition(struct bedInput *bi)
 /* read next set of overlapping beds */
 {
 struct bed3 *bedPart = bedInputNext(bi);
 struct bed3 *bed;
 
 if (bedPart == NULL)
     return NULL;  /* no more */
 /* add more beds while they overlap, due to way input is sorted
  * with by start and then reverse end */
 
-int partCnt = 1; // already have one
 while ((bed = bedInputNext(bi)) != NULL)
     {
-    boolean samePart = isOverlapped(bed, bedPart);
-    if (samePart || ((partCnt < gPartSize) && sameChrom(bed, bedPart)))
+    if (isOverlapped(bed, bedPart))
         {
         bedPart->chromStart = min(bedPart->chromStart, bed->chromStart);
         bedPart->chromEnd = max(bedPart->chromEnd, bed->chromEnd);
         bed3Free(&bed);
-        if (!samePart)
-            partCnt++;
         }
     else
         {
         bedInputPutBack(bi, bed);
         break;
         }
     }
 return bedPart;
 }
 
 static void bedPartition(char *bedFile, char *rangesBed)
 /* split BED files into non-overlapping sets */
 {
 struct bedInput *bi = bedInputNew(bedFile);
 struct bed3 *bedPart;
 FILE *outFh = mustOpen(rangesBed, "w");
-
+int ibed = 0;
 while ((bedPart = readPartition(bi)) != NULL)
     {
-    fprintf(outFh, "%s\t%d\t%d\n", bedPart->chrom, bedPart->chromStart, bedPart->chromEnd);
+    fprintf(outFh, "%s\t%d\t%d\tP%d\n", bedPart->chrom, bedPart->chromStart, bedPart->chromEnd, ibed);
+    ibed++;
     bed3Free(&bedPart);
     }
 carefulClose(&outFh);
 bedInputFree(&bi);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, optionSpecs);
 if (argc != 3)
     usage();
-gPartSize = optionInt("partSize", gPartSize);
+gPartMergeSize = optionInt("partMergeSize", gPartMergeSize);
 gParallel = optionInt("parallel", gParallel);
 bedPartition(argv[1], argv[2]);
 return 0;
 }