Commit d5599559 authored by Alexis  CRISCUOLO's avatar Alexis CRISCUOLO

0.01

parent de7c603a
......@@ -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_.
......
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