bam dedup --in /dev/stdin --out /dev/stdout does not work.

[statgen]

bam dedup --in /dev/stdin --out /dev/stdout does not work.

[mktrost]

What is an sbam? Is that a sorted BAM file?
Here is the wiki documentation on the --in option: http://genome.sph.umich.edu/wiki/BamUtil:_dedup#input_File_.28--in.29
If you want to pass in a BAM file, use --in -.bam
If you want BAM output, use --out -.bam

As of now the code does not automatically determine what type of file you are reading from stdin. It uses the file extension to determine that (defaulting to sam format). Similarly it uses that to determine what type of file you want to write. Samtools alternatively uses -S/-b to help determine that information.

I do not recommend sending both --out and --log to stdout. The output to stdout would be a mix of sam/bam data and logs.

I am very interested in finding out more information about your file written to stdout not being sorted since it is expected to be the same output as if you wrote to a file. It should output reads in the same order that they are in the input file with just a modification to the flag. I would love to recreate this issue and add a test for it to ensure we fix this problem and it doesn't reoccur. Unfortunately, I have not seen this with my own testing. Can you help me to identify the out of order reads (maybe the positions that are out of order).
bam validate --in output1.sam --so_coord
on it? That should let you know if any of the records are unsorted.

Also can you convert output2.sam to a sam file and compare them as sams since that might help figure out what records are out of order.

Thank you for your help in investigating this.