fails with samtools >1.3

[dy7t]

The pipeline hardcodes "samtools sort - " but that usage is deprecated starting with samtools version 1.3. It just prints:

[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]

The fasticlip script seems to just ignore the error and continue.

I recommend you have the script stop if an error happens.
I recommend you explicitly state the version numbers of all the prerequisite programs that you have tested to work with FAST-iCLIP.
You should also give a clearer example of how to test everything by providing a genome FASTA file to be used in the example (rather than just saying to download an unspecified one from ucsc.edu) You should also give the expected results to provide a way to verify the program is operating as expected.

Thanks

[cooleel]

I met the same problem, and samtools version 1.3 seems not good for this software. but the script stopped when it met this issue in my case.
Some of the details are really confusing . Still trying.

Thanks