Biostar234081

##Motivation

convert extended CIGAR to regular CIGAR (https://www.biostars.org/p/234081/)

##Compilation

java compiler SDK 1.8 http://www.oracle.com/technetwork/java/index.html (NOT the old java 1.7 or 1.6) . Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )
GNU Make >= 3.81
curl/wget
git
xsltproc http://xmlsoft.org/XSLT/xsltproc2.html (tested with "libxml 20706, libxslt 10126 and libexslt 815")

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ make biostar234081

by default, the libraries are not included in the jar file, so you shouldn't move them (https://github.com/lindenb/jvarkit/issues/15#issuecomment-140099011 ). You can create a bigger but standalone executable jar by adding standalone=yes on the command line:

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ make biostar234081 standalone=yes

The required libraries will be downloaded and installed in the dist directory.

The a file local.mk can be created edited to override/add some definitions.

For example it can be used to set the HTTP proxy:

http.proxy.host=your.host.com
http.proxy.port=124567

##Synopsis

$ java -jar dist/biostar234081.jar  [options] (stdin|file.bam|file.sam)

Options

-o|--output (OUTPUT-FILE) Output file. Default:stdout.
-formatout|--formatout (FORMAT) output format : sam or bam. if stdout is used Default value : "sam".
-bam_compression_level|--bam_compression_level (LEVEL) BAM Compression level (0-9) Default value : "9".
-h|--help print help
-version|--version show version and exit

##Source Code