ExtendReferenceWithReads

##Motivation

Extending ends of sequences with the help of reads https://www.biostars.org/p/148089/

##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 extendrefwithreads

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 extendrefwithreads 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/extendrefwithreads.jar  [options] (stdin|file)

Options

-o|--output (OUTPUT-FILE) Output file. Default:stdout.
-R|--REF (FASTA) indexed Fasta sequence
-N|--mincontig (VALUE) consider only gaps in reference with size>=N Default value : "100".
-f|--callingfraction (VALUE) (0.0<float<=1.0) new base must have fraction greater than this number Default value : "0.8".
-d|--mindepth (VALUE) min depth Default value : "1".
-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/extendref/ExtendReferenceWithReads.java

Example


$  java   -jar dist/extendrefwithreads.jar \
     -R human_g1k_v37.fasta -f 0.3 \
     f1.bam f2.bam f3.bam 2> /dev/null |\
  cat -n | grep -E '(>|[atgc])' 

     1	>1
   167	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNncgattaccctaacgctcac
   168	cctaaccctcnccctntnccnncnncccnncttcttccgaTAACCCTAACCCTAACCCTA
  3791	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNatt
  3792	tatgcNctttntgctgtGATTCATGGCTGAAATCGTGTTTGACCAGCTATGTGTGTCTCT
  8691	NNNNNNNNNNNNNNNNNNNNNNNNctagGATCCTTGAAGCGCCCCCAAGGGCATCTTCTC
 64089	TGGTGAGGGAAATTAGAACCACGACAATTTGGGAACTTAGCTTCTGCCctgctccNNNNN
 66589	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNgagtAGCTGAGACTAC