19eaeb4d65c6962e516fb23474643ba754c32ea1
angie
  Fri Feb 11 10:52:15 2011 -0800
Feature #2821 (VCF parser): works on a 1000 Genomes pilot release VCF+tabix file with genotypes.[Note: this is a squash of 6 commits, developed off in my vcf branch.]

diff --git src/lib/linefile.c src/lib/linefile.c
index 14e1a5c..d1b888c 100644
--- src/lib/linefile.c
+++ src/lib/linefile.c
@@ -184,72 +184,72 @@
 struct lineFile *lineFileOnString(char *name, bool zTerm, char *s)
 /* Wrap a line file object around string in memory. This buffer
  * have zeroes written into it and be freed when the line file
  * is closed. */
 {
 struct lineFile *lf;
 AllocVar(lf);
 lf->fileName = cloneString(name);
 lf->fd = -1;
 lf->bufSize = lf->bytesInBuf = strlen(s);
 lf->zTerm = zTerm;
 lf->buf = s;
 return lf;
 }
 
-struct lineFile *lineFileOnTabix(char *fileName, bool zTerm)
+struct lineFile *lineFileOnTabix(char *fileOrUrl, bool zTerm)
 /* Wrap a line file around a data file that has been compressed and indexed
- * by the tabix command line program.  The index file <fileName>.tbi must be
- * readable in addition to fileName. If there's a problem, warn & return NULL.
+ * by the tabix command line program.  The index file <fileOrUrl>.tbi must be
+ * readable in addition to fileOrUrl. If there's a problem, warn & return NULL.
  * This works only if kent/src has been compiled with USE_TABIX=1 and linked
  * with the tabix C library. */
 {
 #ifdef USE_TABIX
-int tbiNameSize = strlen(fileName) + strlen(".tbi") + 1;
+int tbiNameSize = strlen(fileOrUrl) + strlen(".tbi") + 1;
 char *tbiName = needMem(tbiNameSize);
-safef(tbiName, tbiNameSize, "%s.tbi", fileName);
-tabix_t *tabix = ti_open(fileName, tbiName);
+safef(tbiName, tbiNameSize, "%s.tbi", fileOrUrl);
+tabix_t *tabix = ti_open(fileOrUrl, tbiName);
 if (tabix == NULL)
     {
-    warn("Unable to open \"%s\"", fileName);
+    warn("Unable to open \"%s\"", fileOrUrl);
     freez(&tbiName);
     return NULL;
     }
 if ((tabix->idx = ti_index_load(tbiName)) == NULL)
     {
     warn("Unable to load tabix index from \"%s\"", tbiName);
     freez(&tbiName);
     return NULL;
     }
 struct lineFile *lf = needMem(sizeof(struct lineFile));
-lf->fileName = cloneString(fileName);
+lf->fileName = cloneString(fileOrUrl);
 lf->fd = -1;
 lf->bufSize = 64 * 1024;
 lf->buf = needMem(lf->bufSize);
 lf->zTerm = zTerm;
 lf->tabix = tabix;
 freez(&tbiName);
 return lf;
 #else // no USE_TABIX
 warn(COMPILE_WITH_TABIX, "lineFileOnTabix");
 return NULL;
 #endif // no USE_TABIX
 }
 
 boolean lineFileSetTabixRegion(struct lineFile *lf, char *seqName, int start, int end)
 /* Assuming lf was created by lineFileOnTabix, tell tabix to seek to the specified region
- * and return TRUE (or if unable, return FALSE). */
+ * and return TRUE (or if there are no items in region, return FALSE). */
 {
 #ifdef USE_TABIX
 if (lf->tabix == NULL)
     errAbort("lineFileSetTabixRegion: lf->tabix is NULL.  Did you open lf with lineFileOnTabix?");
 int tabixSeqId = ti_get_tid(lf->tabix->idx, seqName);
 if (tabixSeqId < 0 && startsWith("chr", seqName))
     // We will get some files that have chr-less Ensembl chromosome names:
     tabixSeqId = ti_get_tid(lf->tabix->idx, seqName+strlen("chr"));
 if (tabixSeqId < 0)
     return FALSE;
 ti_iter_t iter = ti_queryi(lf->tabix, tabixSeqId, start, end);
 if (iter == NULL)
     return FALSE;
 if (lf->tabixIter != NULL)
     ti_iter_destroy(lf->tabixIter);