[Samtools-help] SAM header 'SO:unknown' fails

[Julian G. <jul...@em...>]

Hi,

Can Picard's 'MergeSamFiles' handle a BAM header that specifies 'SO' as 
'unknown'?  This is valid in the current SAM specs 
(http://samtools.sourceforge.net/SAM1.pdf), but seems to break Picard:

[Sat Aug 31 08:46:13 BST 2013] net.sf.picard.sam.MergeSamFiles 
INPUT=[out.bam] OUTPUT=out-sort.bam CREATE_INDEX=true 
SORT_ORDER=coordinate ASSUME_SORTED=false 
MERGE_SEQUENCE_DICTIONARIES=false USE_THREADING=false VERBOSITY=INFO 
QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 
MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false
[Sat Aug 31 08:46:13 BST 2013] Executing as jge...@eb... 
on Linux 2.6.32-358.14.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 
1.6.0_24-b24; Picard version: 1.97(1540)
[Sat Aug 31 08:46:14 BST 2013] net.sf.picard.sam.MergeSamFiles done. 
Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1138294784
To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp
Exception in thread "main" java.lang.IllegalArgumentException: No enum 
const class net.sf.samtools.SAMFileHeader$SortOrder.unknown
	at java.lang.Enum.valueOf(Enum.java:214)
	at net.sf.samtools.SAMFileHeader$SortOrder.valueOf(SAMFileHeader.java:58)
	at net.sf.samtools.SAMFileHeader.getSortOrder(SAMFileHeader.java:239)
	at net.sf.picard.sam.MergeSamFiles.doWork(MergeSamFiles.java:109)
	at 
net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
	at net.sf.picard.sam.MergeSamFiles.main(MergeSamFiles.java:79)

This results from a header line: "@HD	VN:1.0	SO:unknown".  Changing the 
header to "@HD	VN:1.0	SO:unsorted" fixes the problem.

Best wishes
Julian