Currently when iRAP is used to run HISAT2 via irap_single lib the novel splice sites are calculated but not output to the final directory. This PR adds splices to MAPPING_REPORT_PRE_STATS when HISAT2 is the mapper, and gets reported by print_mapping_report_req() for reporting by irap_single_lib.
I've had to work around the usual Make idiosyncracies (single target etc), so I've copied the splicing from the HISAT2 output where it's been implicitly produced.
Currently when iRAP is used to run HISAT2 via irap_single lib the novel splice sites are calculated but not output to the final directory. This PR adds splices to MAPPING_REPORT_PRE_STATS when HISAT2 is the mapper, and gets reported by print_mapping_report_req() for reporting by irap_single_lib.
I've had to work around the usual Make idiosyncracies (single target etc), so I've copied the splicing from the HISAT2 output where it's been implicitly produced.