MergeSamFiles accept SO:UNKNOWN

[MichelMoser]

Bug Report

Affected tool(s)

MergeSamFiles

Affected version(s)

picard2.9.0.jar

Description

IAim is to merge bam files from BLASR alignment which carry the header:
@hd VN:1.5 SO:UNKNOWN pb:3.0.1

right now, this produces the error:

Steps to reproduce

java -jar /home/mmoser/picard2.9.0.jar MergeSamFiles I=10_aligned.bam.bam I=11_aligned.bam.bam I=12_aligned.bam.bam I=13_aligned.bam.bam I=14_aligned.bam.bam I=15_aligned.bam.bam I=16_aligned.bam.bam I=17_aligned.bam.bam I=18_aligned.bam.bam I=19_aligned.bam.bam I=1_aligned.bam.bam I=20_aligned.bam.bam I=21_aligned.bam.bam I=22_aligned.bam.bam O=/data7/users/tural/50smrtcell_sorted.bam VALIDATION_STRINGENCY=SILENT MAX_RECORDS_IN_RAM=50000 TMP_DIR=/data7/users/tural USE_THREADING=true

Expected behavior

Ignore the SO: in the input files and sort them according to coordinates when merging the files.

Actual behavior

Throws error:

Exception in thread "main" java.lang.IllegalArgumentException: No enum constant htsjdk.samtools.SAMFileHeader.SortOrder.UNKNOWN
        at java.lang.Enum.valueOf(Enum.java:238)
        at htsjdk.samtools.SAMFileHeader$SortOrder.valueOf(SAMFileHeader.java:66)
        at htsjdk.samtools.SAMFileHeader.getSortOrder(SAMFileHeader.java:255)
        at picard.sam.MergeSamFiles.doWork(MergeSamFiles.java:161)
        at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:205)
        at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:94)
        at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:104)

Of course, there is a solution of just rewriting the BAM-header but as this is quite timeconsuming for large BAM-files, i wondered if there is an option to ignore the SO value of input files when merging.

Thank you,
Michel

[yfarjoun]

fixed