Biostar78400

##Motivation

add the read group info to the sam file on a per lane basis

##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). And I think htsjdk installs it.
xsltproc http://xmlsoft.org/XSLT/xsltproc2.html (tested with "libxml 20706, libxslt 10126 and libexslt 815")

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ make biostar78400

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 biostar78400 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/biostar78400.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".
-x|--xmlFile (VALUE) XML description of the groups.
-p|--regex (VALUE) Regular expression that can be used to parse read names in the incoming SAM file. Flowcell: (group 1)and the lane (group 2). Another pattern could be '[a-zA-Z0-9\-]+:[0-9]+:([a-zA-Z0-9]+):([0-9]):[0-9]+:[0-9]+:[0-9]+..' (Highseq) Default value : "([a-zA-Z0-9]+):([0-9]):[0-9]+:[0-9]+:[0-9]+.".
-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/biostar/Biostar78400.java

Read names

Reads' name should start with the following signature:

XML

the XML should look like this:

<read-groups>
<flowcell name="HS2000-1259_127">
 <lane index="1">
   <group ID="X1">
     <library>L1</library>
     <platform>P1</platform>
     <sample>S1</sample>
     <platformunit>PU1</platformunit>
     <center>C1</center>
     <description>blabla</description>
   </group>
 </lane>
</flowcell>
<flowcell name="HS2000-1259_128">
 <lane index="2">
   <group ID="x2">
     <library>L2</library>
     <platform>P2</platform>
     <sample>S2</sample>
     <platformunit>PU1</platformunit>
     <center>C1</center>
     <description>blabla</description>
   </group>
 </lane>
</flowcell>
</read-groups>

Example


$ cat input.sam 
@SQ SN:ref  LN:45
@SQ SN:ref2 LN:40
HS2000-1259_127:1:1210:15640:52255  163 ref 7   30  8M4I4M1D3M  =   37  39  
TTAGATAAAGAGGATACTG *   XX:B:S,12561,2,20,112
HS2000-1259_128:2:1210:15640:52255  0   ref 9   30  1S2I6M1P1I1P1I4M2I  *   0   
0   AAAAGATAAGGGATAAA   *

$java -jar dist/biostar78400.jar \
    -x groups.xml \
    input.sam \
   

@HD VN:1.4  SO:unsorted
@SQ SN:ref  LN:45
@SQ SN:ref2 LN:40
@RG ID:X1   PL:P1   PU:P1   LB:L1   DS:blabla   SM:S1   CN:C1
@RG ID:x2   PL:P2   PU:P2   LB:L2   DS:blabla   SM:S2   CN:C1
@PG ID:Biostar78400 PN:Biostar78400 PP:Biostar78400 VN:1.0  (...)
HS2000-1259_127:1:1210:15640:52255  163 ref 7   30  8M4I4M1D3M  =   37  39  TTAGATAAAGAGGATACTG *   RG:Z:X1 XX:B:S,12561,2,20,112
HS2000-1259_128:2:1210:15640:52255  0   ref 9   30  1S2I6M1P1I1P1I4M2I  *   0   0AAAAGATAAGGGATAAA  *   RG:Z:x2