From 0a3bf89715283e4d322d28ba4147e987e3477ee3 Mon Sep 17 00:00:00 2001
From: Charles Plessy <plessy@debian.org>
Date: Thu, 19 Aug 2010 15:49:27 +0900
Subject: [PATCH] Imported Upstream version 0.1.2

---
 index.c | 8 ++++----
 main.c  | 2 +-
 tabix.1 | 6 +++---
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/index.c b/index.c
index 80b863d..704b037 100644
--- a/index.c
+++ b/index.c
@@ -158,7 +158,7 @@ static int get_intv(ti_index_t *idx, kstring_t *str, ti_intv_t *intv)
 				intv->tid = get_tid(idx, str->s + b);
 				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.
+				// here ->beg is 0-based.
 				intv->beg = intv->end = strtol(str->s + b, &s, 0);
 				if (!(idx->conf.preset&TI_FLAG_UCSC)) --intv->beg;
 			} else {
@@ -174,7 +174,7 @@ static int get_intv(ti_index_t *idx, kstring_t *str, ti_intv_t *intv)
 							if (op == 'M' || op == 'D' || op == 'N') l += x;
 							s = t + 1;
 						}
-						intv->end = intv->beg + l - 1;
+						intv->end = intv->beg + l;
 					}
 				} else if ((idx->conf.preset&0xffff) == TI_PRESET_VCF) {
 					// FIXME: the following is NOT tested and is likely to be buggy
@@ -188,7 +188,7 @@ static int get_intv(ti_index_t *idx, kstring_t *str, ti_intv_t *intv)
 								s = t + 1;
 							} else ++s;
 						}
-						intv->end = intv->beg + max - 1;
+						intv->end = intv->beg + max;
 					}
 				}
 			}
@@ -197,7 +197,7 @@ static int get_intv(ti_index_t *idx, kstring_t *str, ti_intv_t *intv)
 		}
 	}
 	if (intv->tid < 0 || intv->beg < 0 || intv->end < 0) return -1;
-	intv->bin = ti_reg2bin(intv->beg-1, intv->end);
+	intv->bin = ti_reg2bin(intv->beg, intv->end);
 	return 0;
 }
 
diff --git a/main.c b/main.c
index 02daedf..a227192 100644
--- a/main.c
+++ b/main.c
@@ -5,7 +5,7 @@
 #include "bgzf.h"
 #include "tabix.h"
 
-#define PACKAGE_VERSION "0.1.1 (r542)"
+#define PACKAGE_VERSION "0.1.2 (r543)"
 
 static int fetch_func(int l, const char *s, void *data)
 {
diff --git a/tabix.1 b/tabix.1
index 4b5eea2..aa6dc75 100644
--- a/tabix.1
+++ b/tabix.1
@@ -69,8 +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. The end column can be the same as
-start column, [5]
+Column of end chromosomal position. The end column can be the same as the
+start column. [5]
 .TP
 .BI "-S " INT
 Skip first INT lines in the data file. [0]
@@ -84,7 +84,7 @@ rather than 1-based.
 .RE
 
 .SH EXAMPLE
-grep -v ^"#" unsorted.gff | sort -k1,1 -k4,4n | bgzip -c > sorted.gff.gz;
+(grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip > sorted.gff.gz;
 
 tabix -p gff sorted.gff.gz;
 
-- 
2.30.2