Increment version & update reference

docs/reference/command_line/check.txt

@@ -2,7 +2,7 @@ $ rnftools check -h
 
 usage: rnftools check [-h]
 
-Check if RNFtools and SMBL are up-to-date.
+Check if RNFtools are up-to-date.
 
 optional arguments:
   -h, --help  show this help message and exit

docs/reference/command_line/dwgsim2rnf.txt

@@ -1,6 +1,6 @@
 $ rnftools dwgsim2rnf -h
 
-usage: rnftools dwgsim2rnf [-h] [-p str] [-e] -o file -x file [-g int] [-u]
+usage: rnftools dwgsim2rnf [-h] -p str [-e] -o file -x file [-g int]
 
 Convert a DwgSim FASTQ file (dwgsim_prefix.bfast.fastq) to RNF-FASTQ.
 
@@ -17,4 +17,3 @@ optional arguments:
                         input). It can be created using 'samtools faidx'.
   -g int, --genome-id int
                         Genome ID in RNF (default: 1).
-  -u, --allow-unmapped  Allow unmapped reads.

docs/reference/command_line/main.txt

@@ -4,12 +4,12 @@ usage: rnftools [-h]
                 {,check,publication,validate,liftover,sam2rnf,art2rnf,curesim2rnf,dwgsim2rnf,mason2rnf,wgsim2rnf,merge,sam2es,es2et,et2roc,sam2roc}
                 ...
 
-================================================
-RNFtools -  http://rnftools.rtfd.org
-------------------------------------
-version: 0.2.2
+==================================================
+RNFtools -  http://karel-brinda.github.io/rnftools
+--------------------------------------------------
+version: 0.3.1.1
 contact: Karel Brinda (karel.brinda@univ-mlv.fr)
-================================================
+==================================================
 
 positional arguments:
   {,check,publication,validate,liftover,sam2rnf,art2rnf,curesim2rnf,dwgsim2rnf,mason2rnf,wgsim2rnf,merge,sam2es,es2et,et2roc,sam2roc}

docs/reference/command_line/merge.txt

@@ -11,8 +11,8 @@ optional arguments:
   -o out            output prefix
 
 Source RNF-FASTQ files should satisfy the following conditions:
-   1) Each file contains only reads corresponding to one genome (with the 
-      same genome id).
-   2) All files contain reads of the same type (single-end / paired-end).
-   3) Reads with more reads per tuple (e.g., paired-end) have '/1', etc.
-      in suffix (for identification of nb of read).
+	1) Each file contains only reads corresponding to one genome (with the
+	   same genome id).
+	2) All files contain reads of the same type (single-end / paired-end).
+	3) Reads with more reads per tuple (e.g., paired-end) have '/1', etc.
+	   in suffix (for identification of nb of read).

rnftools/version.py

@@ -1 +1 @@
-VERSION = "0.3.1.0"
+VERSION="0.3.1.1"