e70152e44cc66cc599ff6b699eb8adc07f3e656a
kent
  Sat May 24 21:09:34 2014 -0700
Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
diff --git src/hg/lib/chromInserts.c src/hg/lib/chromInserts.c
index cae6768..aef386b 100644
--- src/hg/lib/chromInserts.c
+++ src/hg/lib/chromInserts.c
@@ -1,93 +1,96 @@
 /* chromInserts - this module helps handle centromeres, heterochromatic regions
  * and other large gaps in chromosomes. */
 
+/* Copyright (C) 2014 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+
 #include "common.h"
 #include "hash.h"
 #include "linefile.h"
 #include "chromInserts.h"
 
 
 static char *dashIsNull(char *s)
 /* Return cloned copy of string, or NULL if it's just a dash. */
 {
 if (sameString(s, "-"))
     return NULL;
 else
     return cloneString(s);
 }
 
 struct chromInserts *chromInsertsRead(char *fileName, struct hash *insertsHash)
 /* Read in inserts file and process it. */
 {
 struct chromInserts *chromInsertsList = NULL, *chromInserts;
 struct bigInsert *insert;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *words[16], *chrom;
 int wordCount;
 struct hashEl *hel;
 
 while ((wordCount = lineFileChop(lf, words)) != 0)
     {
     lineFileExpectWords(lf, 5, wordCount);
     chrom = words[0];
     if ((chromInserts = hashFindVal(insertsHash, chrom)) == NULL)
         {
 	AllocVar(chromInserts);
 	hel = hashAdd(insertsHash, chrom, chromInserts);
 	chromInserts->chrom = hel->name;
 	slAddHead(&chromInsertsList, chromInserts);
 	}
     AllocVar(insert);
     insert->ctgBefore = dashIsNull(words[1]);
     insert->ctgAfter = dashIsNull(words[2]);
     insert->size = atoi(words[3]);
     insert->type = cloneString(words[4]);
     if (insert->ctgAfter == NULL)
         chromInserts->terminal = insert;
     else
         {
 	slAddTail(&chromInserts->insertList, insert);
 	}
     insert->chrom = chromInserts;
     }
 lineFileClose(&lf);
 slReverse(&chromInsertsList);
 return chromInsertsList;
 }
 
 struct bigInsert *bigInsertBeforeContig(struct chromInserts *chromInserts, 
 	char *contig)
 /* Return the big insert (if any) before contig) */
 {
 struct bigInsert *bi;
 if (chromInserts == NULL)
     return NULL;
 for (bi = chromInserts->insertList; bi != NULL; bi = bi->next)
     {
     if (sameString(bi->ctgAfter, contig))
         return bi;
     }
 return NULL;
 }
 
 static int chromInsertsDefaultGapSize = 200000;
 
 void chromInsertsSetDefaultGapSize(int size)
 /* Set default gap size. */
 {
 chromInsertsDefaultGapSize = size;
 }
 
 int chromInsertsGapSize(struct chromInserts *chromInserts, char *contig, boolean isFirst)
 /* Return size of gap before next contig. */
 {
 int size = (isFirst ? 0 : chromInsertsDefaultGapSize);
 if (chromInserts != NULL)
     {
     struct bigInsert *bi = bigInsertBeforeContig(chromInserts, contig);
     if (bi != NULL)
         size = bi->size;
     }
 return size;
 }