Biostar78400

##Motivation Add the read group info to the sam file on a per lane basis

Compilation

See also Compilation.

$ make biostar78400

##Options

Option	Description
IN=File	BAM file to process (or stdin). Default value: null.
OUT=File	BAM file (or stdout). Default value: null.
XML=File	XML desfription of the groups. See below Required.

XML config

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 \
	XML=groups.xml \
	I=input.sam \
 	VALIDATION_STRINGENCY=LENIENT

@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