ChimPipe version 0.8.8

New features

• Pipeline able to take a bam file as input. Now it has two running modes: FASTQ and BAM as input.
• Modifications in the way to run the pipeline and in the output directory structure to make it more flexible, clear and avoid some problems.
• Pipeline configuration displayed in a clearer way.
• Decreased the false positive rate. Remap only those multi-mappings with more than 10 hits instead of all the multi-mappings. This was leading to some false positives arising from alignment artifacts.

Bug fixes

• Fixed a bug when an output directory is specified. Wrote in the cwd instead of the desired directory.
• Fixed a problem in the step to extract mappings to remap in the second mapping phase. Missed alignments with 5 edit distance.
• Fixed problem with reads split-mapping without canonical splice sites. Program was producing wrong formatted chimeras file.