BamLiftOver

##Motivation

Lift-over a BAM file.

##Compilation

Requirements / Dependencies

Since 2016-05-30 the compilation of the "Java API for high-throughput sequencing data (HTS) formats" (htsjdk) library requires gradle http://gradle.org

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
gradle http://gradle.org is only required to compile the "Java API for high-throughput sequencing data (HTS) formats" (htsjdk)
xsltproc http://xmlsoft.org/XSLT/xsltproc2.html

Download and Compile

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

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 addinging standalone=yes on the command line:

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

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

edit 'local.mk' (optional)

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

to set the gradle user home ( https://docs.gradle.org/current/userguide/build_environment.html#sec:gradle_properties_and_system_properties )

gradle.user.home=/dir1/dir2/gradle_user_home

##Synopsis

$ java -jar dist/bamliftover.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".
-f|--chain (VALUE) LiftOver file. Require
-m|--minmatch (VALUE) lift over min-match. default:-1 == use default value from htsjdk LiftOver.DEFAULT_LIFTOVER_MINMATCH Default value : "-1".
-D|--reference (VALUE) indexed REFerence file for the new sequence dictionary. Required
-h|--help print help
-version|--version show version and exit

##Source Code

Main code is: https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/liftover/BamLiftOver.java