README and version updated to 1.1.0

README.md

@@ -73,8 +73,9 @@ ntcard [OPTIONS] ... [FILE]
 Parameters:
   * `-k`,  `--kmer=SIZE`: the length of *k*-mer `[64]`
   * `-t`,  `--threads=N`: use N parallel threads `[1]`
-  * `-c`,  `--cov=N`: the maximum coverage of *k*-mer in output `[64]`
-  * `-p`,  `--pref=STRING`: the prefix for output file name `[freq]`
+  * `-c`,  `--cov=N`: the maximum coverage of *k*-mer in output `[1000]`
+  * `-p`,  `--pref=STRING`: the prefix for output file names `[freq]`
+  * `-o`,  `--output=STRING`: the name for single output file name (can be used only for single compact output file)`
   * `FILE`: input file or set of files seperated by space, in fasta, fastq, sam, and bam formats. The files can also be in compressed (`.gz`, `.bz2`, `.xz`) formats . A list of files containing file names in each row can be passed with `@` prefix.
 
 For example to run ntcard on a test file `reads.fastq` with `k=50`:

configure.ac

@@ -1,5 +1,5 @@
 AC_PREREQ(2.62)
-AC_INIT(NTCARD, 1.0.1, hmohamadi@bcgsc.ca, ntcard,
+AC_INIT(NTCARD, 1.1.0, hmohamadi@bcgsc.ca, ntcard,
 		https://github.com/bcgsc/ntCard)
 # add 'foreign' to allow README.md instead of README
 AM_INIT_AUTOMAKE([foreign subdir-objects])

ntcard.cpp

@@ -18,7 +18,7 @@
 #define PROGRAM "ntcard"
 
 static const char VERSION_MESSAGE[] =
-    PROGRAM " Version 1.0.2 \n"
+    PROGRAM " Version 1.1.0 \n"
     "Written by Hamid Mohamadi.\n"
     "Copyright 2018 Canada's Michael Smith Genome Science Centre\n";
 

nthll.cpp

@@ -18,9 +18,9 @@
 #define PROGRAM "nthll"
 
 static const char VERSION_MESSAGE[] =
-    PROGRAM " Version 1.0.0 \n"
+    PROGRAM " Version 1.1.0 \n"
     "Written by Hamid Mohamadi.\n"
-    "Copyright 2016 Canada's Michael Smith Genome Science Centre\n";
+    "Copyright 2018 Canada's Michael Smith Genome Science Centre\n";
 
 static const char USAGE_MESSAGE[] =
     "Usage: " PROGRAM " [OPTION]... FILES...\n"