0.01

README.md

@@ -21,16 +21,13 @@ The source code of _SAM2MSA_ is inside the _src_ directory and can be compiled a
 On computers with [Oracle JDK](http://www.oracle.com/technetwork/java/javase/downloads/index.html) (8 or higher) installed, Java executable jar files can be created. 
 In a command-line window, go to the _src_ directory and type:
 ```bash
-javac SAM2MAP.java 
-echo Main-Class: SAM2MAP > MANIFEST.MF 
-jar -cmvf MANIFEST.MF SAM2MAP.jar SAM2MAP.class 
-javac MAP2FASTA.java 
-echo Main-Class: MAP2FASTA > MANIFEST.MF 
-jar -cmvf MANIFEST.MF MAP2FASTA.jar MAP2FASTA.class 
-javac FASTA2MSA.java 
-echo Main-Class: FASTA2MSA > MANIFEST.MF 
-jar -cmvf MANIFEST.MF FASTA2MSA.jar FASTA2MSA.class 
-rm MANIFEST.MF SAM2MAP.class MAP2FASTA.class FASTA2MSA.class 
+for p in SAM2MAP MAP2FASTA FASTA2MSA
+do
+  javac $p.java ;
+  echo Main-Class: $p > MANIFEST.MF ;
+  jar -cmvf MANIFEST.MF $p.jar $p.class ;
+  rm MANIFEST.MF $p.class ;
+done
 ```
 This will create the three executable jar files `SAM2MAP.jar`, `MAP2FASTA.jar` and `FASTA2MSA.jar` that can be run with the following command line models:
 ```bash
@@ -44,13 +41,12 @@ java -jar FASTA2MSA.jar [options]
 On computers with [GraalVM](hhttps://www.graalvm.org/downloads/) installed, native executables can also be built. 
 In a command-line window, go to the _src_ directory, and type:
 ```bash
-javac SAM2MAP.java 
-native-image SAM2MAP SAM2MAP
-javac MAP2FASTA.java 
-native-image MAP2FASTA MAP2FASTA
-javac FASTA2MSA.java 
-native-image FASTA2MSA FASTA2MSA
-rm SAM2MAP.class MAP2FASTA.class FASTA2MSA.class 
+for p in SAM2MAP MAP2FASTA FASTA2MSA
+do
+  javac $p.java ;
+  native-image $p $p ;
+  rm $p.class ;
+done
 ```
 This will create the three native executable `SAM2MAP`, `MAP2FASTA` and `FASTA2MSA` that can be launched with the following command line models:
 ```bash
@@ -380,11 +376,11 @@ The directory _example/_ contains the three output files written by _SAM2MAP_ fo
 
 #### _FASTA2MSA_ on consensus sequences
 
-The following command line create a MSA using _FASTA2MSA_ on the 38 generated consensus sequences (the input file _infile.txt_ is available _example/_):
+The following command line create a MSA using _FASTA2MSA_ on the 38 generated consensus sequences (the input file _infile.txt_ is available in _example/_):
 ```bash
 FASTA2MSA -i infile.txt -o msa -g CH16.gff -v
 ```
-The directory _example/_ contains the tow output files written by _FASTA2MSA_:
+The directory _example/_ contains the two output files written by _FASTA2MSA_:
 * _msa.fasta.gz_: a multiple sequence alignment of 8,371,282 aligned nucleotide characters in gziped FASTA format,
 * _msa.var.tsv_: a tab-delimited file summarizing the 489 variable characters inside _msa.fasta_.