Imported Upstream version 0.1.1

diff --git a/index.c b/index.c
index cc564981ee5696f0d3350298312287c516946f85..80b863d3f84d53ea4c8eafb612db56150c94870a 100644 (file)
--- a/index.c
+++ b/index.c
@@ -159,8 +159,8 @@ static int get_intv(ti_index_t *idx, kstring_t *str, ti_intv_t *intv)
                                if (i != str->l) str->s[i] = '\t';
                        } else if (id == idx->conf.bc) {
                                // here ->beg is 1-based. it will be changed to 0-based at the end of this routine.
-                               intv->beg = strtol(str->s + b, &s, 0);
-                               if (idx->conf.preset&TI_FLAG_UCSC) ++intv->beg;
+                               intv->beg = intv->end = strtol(str->s + b, &s, 0);
+                               if (!(idx->conf.preset&TI_FLAG_UCSC)) --intv->beg;
                        } else {
                                if ((idx->conf.preset&0xffff) == TI_PRESET_GENERIC) {
                                        if (id == idx->conf.ec) intv->end = strtol(str->s + b, &s, 0);

diff --git a/main.c b/main.c
index faef7fbcfcd2cfba03b104c17d3678fbeb90c527..02daedf80d2b7894ecfa656314290f123e89fbc2 100644 (file)
--- a/main.c
+++ b/main.c
@@ -5,7 +5,7 @@
 #include "bgzf.h"
 #include "tabix.h"
 
-#define PACKAGE_VERSION "0.1.0 (r506)"
+#define PACKAGE_VERSION "0.1.1 (r542)"
 
 static int fetch_func(int l, const char *s, void *data)
 {
@@ -82,6 +82,7 @@ int main(int argc, char *argv[])
                        for (i = optind + 1; i < argc; ++i) {
                                int tid, beg, end;
                                if (ti_parse_region(idx, argv[i], &tid, &beg, &end) == 0) {
+                                       fprintf(stderr, "%d,%d\n", beg, end);
                                        ti_fetch(fp, idx, tid, beg, end, 0, fetch_func);
                                } else fprintf(stderr, "[main] invalid region: unknown target name or minus interval.\n");
                        }

diff --git a/tabix.1 b/tabix.1
index 6b6e2d686adf10a4a02a8ae6f8e7780fa86af4c5..4b5eea25057be28b6a7fa749ef2272a14ebfb313 100644 (file)
--- a/tabix.1
+++ b/tabix.1
@@ -1,4 +1,4 @@
-.TH tabix 1 "2 November 2009" "tabix-0.1.0" "Bioinformatics tools"
+.TH tabix 1 "16 March 2009" "tabix-0.1.1" "Bioinformatics tools"
 .SH NAME
 .PP
 bgzip - Block compression/decompression utility
@@ -69,7 +69,8 @@ are all stored in the index file and thus not used in data retrieval. [1]
 Column of start chromosomal position. [4]
 .TP
 .BI "-e " INT
-Column of end chromosomal position. [5]
+Column of end chromosomal position. The end column can be the same as
+start column, [5]
 .TP
 .BI "-S " INT
 Skip first INT lines in the data file. [0]