support for samtools > 1.2

[gedankenstuecke]

When running circlator with samtools 1.3 the mapping step failed due to the error below. This is because starting from samtools 1.3 you have to specify the -o option for the output-file, otherwise it will not run. You can already start using this parameter from version 1.2 on.

As an easy workaround I now just checked for the version of samtools before running the sort-step and either run it with or without the -o flag.

The following command failed with exit code 1
samtools sort -@ 1 -m 500M 01.mapreads.bam.tmp.unsorted.bam 01.mapreads

The output was:

[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files
Usage: samtools sort [options...] [in.bam]
Options:
  -l INT     Set compression level, from 0 (uncompressed) to 9 (best)
  -m INT     Set maximum memory per thread; suffix K/M/G recognized [768M]
  -n         Sort by read name
  -o FILE    Write final output to FILE rather than standard output
  -T PREFIX  Write temporary files to PREFIX.nnnn.bam
  -@, --threads INT
             Set number of sorting and compression threads [1]
      --input-fmt-option OPT[=VAL]
               Specify a single input file format option in the form
               of OPTION or OPTION=VALUE
  -O, --output-fmt FORMAT[,OPT[=VAL]]...
               Specify output format (SAM, BAM, CRAM)
      --output-fmt-option OPT[=VAL]
               Specify a single output file format option in the form
               of OPTION or OPTION=VALUE
      --reference FILE
               Reference sequence FASTA FILE [null]

[martinghunt]

Thanks for reporting this, and the fix. Code looks fine to me.

Travis CI is complaining when trying to install pysam, but that's unrelated to your changes. I'll need to fix that before merging...

[gedankenstuecke]

Thanks, glad you can use the changes! On my end all tests succeeded, but then I did see that there are none so far for the mapping step.

Right now I'm running it on a small test-set on my end to see whether the changes run through fine.

[martinghunt]

Hmm, you're right. I will also complete the unit tests for the mapping. I left placeholders for them but haven't filled them in yet.

[gedankenstuecke]

Great, I'll keep you posted on how it works on my end until then. 😃

[gedankenstuecke]

Okay, that worked well on my end 👍 If I can be of any help for writing the tests, let me know :-)

[martinghunt]

Great, thanks for the update. I'll merge your PR, then do the Travis fix and add unit tests, and make a new release...

[gedankenstuecke]

Great, thanks so much!