ISMapper v2.0.2

Updated ISMapper to remove the requirement for Bio.Alphabet, so is now compatible with later versions of BioPython.

ISMapper 2.0.1

Merged bugfix for issue #38, this release will address issue #40

ISMapper v2.0

ISMapper version 2 now supports only 'typing' mode - detecting IS sites relative to a reference genome.
ISMapper is now compatible with Python 3 (and only Python 3).

The code has been restructured to (hopefully!) make it easier to debug when issues arise.

ISMapper v0.1.5.2

Pull request incorporated which fixes issue #31

ISMapper v0.1.5.1

Small fix that updates the slurm scripts.

ISMapper v0.1.5

• ISMapper now works with all current versions of SAMtools (Issue #11, thanks to Anders Gonçalves da Silva for the fix)
• Deletion of intermediate files when no hits are found (Issue #10, thanks to Ryan Wick for this fix)
• Multiple query sequences must now be supplied using a multi-entry fasta file (Issue #9)
• ISMapper now catches segmentation fault errors thrown by Bedtools when one or more bedfiles are empty (Issue #16, Issue #19)
• Documentation now provides link to published paper (Issue #22)
• SLURM script no longer prints that it was unable to run the following samples if there are no samples that were unable to run
• compiled_table.py now does a final check for any overlapping positions, and merges them if necessary
• --output flag no longer required, if not supplied the prefix will default to the current date and time (format: ddmmyy_hourMinute)

ISMapper v0.1.4

Wed 7 Oct 2015

• can now supply output directory using --directory command
• can now ask BWA to use multiple threads using --t command
• fixed some cases where an unpaired hit would pair incorrectly with itself
• correct distances returned if the flanking gene should be the first or last
  gene in the reference
• fixed an error where no hits reported but bed files are non-empty
• possible related IS call must now meet 50% ID and 50% coverage threshold
  otherwise the hit is discarded

ISMapper v0.1.3

Mon 10 Aug 2015

• fixed soft clipped read selection (Special thanks to Katie Cox for helping with this one)
• bam files now deleted by default, can be kept using the --bam flag
• IGV compatible bed files now created if --igv flag used (again thanks to Katie Cox)

ISMapper v0.1.2

Mon 18 May 2015

• removed functional prediction as currently buggy
• corrected some intermediate file names