errer when generating path for IGV Tools "sort"

[JoaquinArino]

Dear colleagues, I started using IGV a few weks ago and recently started using the IGV tools "Sort" from the IGV interface (version 2.2.13). I observe what it seems to be a bug in the proposed path for the output file. For instance, if I select as input file

E:\bowtie2-2.1.0\ChiP01\SAMs\B1.sam the automatic output selection is:

E:\bowtie2-2.sorted.1.0\ChiP01\SAMs\B1.sam Note that this output path refers to a non-existent folder (bowtie2-2.sorted.1.0). If I accept this the system throws an exception when starts running. It seems that the word "sorted" should be placed in the file name (i.e. B1_sorted.sam). If I do this manually , it works. This is not an enormous problem, but it takes a while before one realizes the origin of the trouble (particularly if you are not an expert, as it is my case) and complicates handling of many files. I trust it should be not difficult for you to solve. On the other hand, I congratulate you for this excellent and extremely useful piece of software. Sincerely, Joaquin Arino

[jsilter]

Thanks for the report. This is actually already fixed in the master branch, just hasn't been released yet.

[JoaquinArino]

Great!. Thank you very much. Joaquin

El 05/04/2013 15:45, Jacob Silterra escribió:

Thanks for the report. This is actually already fixed in the master branch, just hasn't been released yet.

— Reply to this email directly or view it on GitHub https://github.com/broadinstitute/IGV/issues/40#issuecomment-15956309.

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Dr. Joaquin Arino Yeast Molecular Biology Laboratory Institut de Biotecnología i Biomedicina Dept. Bioquimica y Biologia Molecular Universitat Autonoma Barcelona Cerdanyola del Vallès 08193, Barcelona, Spain Phone: 34-93-5812182 FAX: 34-93-5812011 WEB: http://grupsderecerca.uab.cat/gbml/es