change

Author: smortezah

README.md

@@ -135,13 +135,13 @@ method is not recommended, but if you tend to use it, it would be a better
 practice to choose a "strong password".
 
 A strong password:
-  * has at least 12 characters;
-  
-  * includes lowercase letters (a-z), uppercase letters (A-Z), digits (0-9) and
-  symbols (e.g. !, #, $, % and });
+*  has at least 12 characters;
+
+*  includes lowercase letters (a-z), uppercase letters (A-Z), digits (0-9) and
+   symbols (e.g. !, #, $, % and });
 
-  * is not a character repetition (e.g. zzzzzz), keyboard pattern (e.g. qwerty)
-  or digit sequences (e.g. 123456).
+*  is not a character repetition (e.g. zzzzzz), keyboard pattern (e.g. qwerty)
+   or digit sequences (e.g. 123456).
 
 The second method to make a key file is using the "keygen" program, which 
 automatically provides a strong password. Running
@@ -154,7 +154,7 @@ Enter a password, then press 'Enter':
 ```
 After typing a raw password, e.g. "A keygen raw pass!", and pressing "Enter",
 the following message appears:
-```
+```text
 Enter a file name to save the generated key, then press 'Enter':
 ```
 The automatically generated strong password will be saved in the file that you
@@ -176,19 +176,19 @@ and
 
 ## CITE
 Please cite the followings, if you use Cryfa:
-  * M. Hosseini, D. Pratas and A.J. Pinho, "Cryfa: a secure encryption tool for genomic
-  data,"*Bioinformatics*, bty645, 2018.
+*  M. Hosseini, D. Pratas and A.J. Pinho, "Cryfa: a secure encryption tool for
+   genomic data, "*Bioinformatics*, bty645, 2018.
 
-  * D. Pratas, M. Hosseini and A.J. Pinho, "Cryfa: a tool to compact and encrypt
-  FASTA files," *11'th International Conference on Practical Applications of 
-  Computational Biology & Bioinformatics* (PACBB), Springer, June 2017.
+*  D. Pratas, M. Hosseini and A.J. Pinho, "Cryfa: a tool to compact and encrypt
+   FASTA files," *11'th International Conference on Practical Applications of 
+   Computational Biology & Bioinformatics* (PACBB), Springer, June 2017.
 
 ## RELEASES
-  * [Release](https://github.com/pratas/cryfa/releases) 2: Secure encryption of
-  FASTA/FASTQ/VCF/SAM/BAM PLUS compacting FASTA/FASTQ.
+*  [Release](https://github.com/pratas/cryfa/releases) 2: Secure encryption of
+   FASTA/FASTQ/VCF/SAM/BAM PLUS compacting FASTA/FASTQ.
 
-  * [Release](https://github.com/pratas/cryfa/releases) 1: Encryption PLUS compacting
-  FASTA.
+*  [Release](https://github.com/pratas/cryfa/releases) 1: Encryption PLUS compacting
+   FASTA.
 
 ## ISSUES
 Please let us know if there is any 

script/res_comp.sh

@@ -52,7 +52,7 @@ function compDecompRes
 
     ### Verify if the decompressed and the original files are equal
     v_file="$result/${1}_V__${dName}_$ft"
-    if [[ -e $v_file ]]; then  V=$(cat $v_file | wc -l);  fi
+    if [[ -e $v_file ]]; then  V=$(wc -l $v_file);  fi
 
     ### Remove extra files
     for xf in $cs_file $cm_file $dm_file; do

script/res_comp_enc.sh

@@ -84,7 +84,7 @@ function compEncDecDecompRes
 
     ### Verify if the decompressed and the original files are equal
     v_file="$result/${1}_${2}_V__${dName}_$ft"
-    if [[ -e $v_file ]]; then  V=$(cat $v_file | wc -l);  fi
+    if [[ -e $v_file ]]; then  V=$(wc -l $v_file);  fi
 
     ### Remove extra files
     for xf in $cs_file $cm_file $dem_file $dm_file $enm_file $ens_file; do

script/res_cryfa_thr.sh

@@ -50,7 +50,7 @@ function cryfaThrRes
 
         ### Verify if the decompressed and the original files are equal
         v_file="$result/${1}_${nThr}_V__${2}_$3"
-        if [[ -e $v_file ]]; then  V=$(cat $v_file | wc -l);  fi
+        if [[ -e $v_file ]]; then  V=$(wc -l $v_file);  fi
 
         ### Remove extra files
         for xf in $cs_file $cm_file $dm_file; do

script/res_enc.sh

@@ -24,7 +24,7 @@ function encDecRes
 
     ### Encrypted file size
     ens_file="$result/${1}_EnS__${dName}_$ft"
-    if [[ -e $ens_file ]]; then  EnS=$(cat $ens_file | awk '{ print $5; }');  fi
+    if [[ -e $ens_file ]]; then  EnS=$(awk '{ print $5; }' $ens_file);  fi
 
     ### Encryption time -- real - user - system
     ent_file="$result/${1}_EnT__${dName}_$ft"