diff --git a/configure.bioconda.ac b/configure.bioconda.ac
index 45147e4..29dd3a7 100644
--- a/configure.bioconda.ac
+++ b/configure.bioconda.ac
@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.63])
-AC_INIT(rnabridge-align, 1.0.0, shaomingfu@gmail.com)
+AC_INIT(rnabridge-align, 1.0.1, shaomingfu@gmail.com)
 AM_INIT_AUTOMAKE()
 AC_CONFIG_SRCDIR([src/main.cc])
 AC_CONFIG_HEADERS([config.h])
diff --git a/configure.linux.ac b/configure.linux.ac
index ca6392d..38fac23 100644
--- a/configure.linux.ac
+++ b/configure.linux.ac
@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.63])
-AC_INIT(rnabridge-align, 1.0.0, shaomingfu@gmail.com)
+AC_INIT(rnabridge-align, 1.0.1, shaomingfu@gmail.com)
 AM_INIT_AUTOMAKE()
 AC_CONFIG_SRCDIR([src/main.cc])
 AC_CONFIG_HEADERS([config.h])
diff --git a/configure.mac.ac b/configure.mac.ac
index b1a172c..80057de 100644
--- a/configure.mac.ac
+++ b/configure.mac.ac
@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.69])
-AC_INIT(rnabridge-align, 1.0.0, shaomingfu@gmail.com)
+AC_INIT(rnabridge-align, 1.0.1, shaomingfu@gmail.com)
 AM_INIT_AUTOMAKE()
 AC_CONFIG_SRCDIR([src/main.cc])
 AC_CONFIG_HEADERS([config.h])
diff --git a/src/config.cc b/src/config.cc
index d7f2349..7b0ede7 100644
--- a/src/config.cc
+++ b/src/config.cc
@@ -95,7 +95,7 @@ bool output_tex_files = false;
 string fixed_gene_name = "";
 int batch_bundle_size = 100;
 int verbose = 1;
-string version = "v1.0.0";
+string version = "v1.0.1";
 
 int parse_arguments(int argc, const char ** argv)
 {