Updated by Jelena 11:30 21/Oct/2017

Send all confusion and weird things to jelena__telenius__at__gmail__com ( and if needed, she will forward them to James )


CB5 CS5 CF5 - CCseqBasic5

BUGS / NON-STANDARD BEHAVIOR :

- Oligo names containing words "RAW" or "FILTERED" or "PREfiltered" may generate the data hubs wrong.


INSTABILITY ISSUES :

- Non-illumina-standard read names may still crash the pipe (this is not necessary, and can be fixed).

- Still unexpected "empty output" without error messages sometimes, when ccanalyser faces wrongly given input.
- Does not kill the script properly when any of the underlying scripts fail.
- Only checks for output files, and not even that for the last script (CCanalyser).


DEVELOPMENT TARGETS :

1) Oligo-file auto-generator (to auto-extend to RE boundary)
2) Dividing the output logs to 4 files : runtime log, runtime error, run results statistics (compact), run results statistics (very detailed)
3) Providing a test data set with its output files - for new users to test that they get the same results
4) Adding facets from log files to the MIG output (counter values which are now only exported to logs/debugging files)
5) Ensuring the SNP behave the same way than non-SNP run (consistency to the duplicate capture reporting)
6) Better user manual - to add the interpretation of the data hub tracks and data to the manual.

7) Better crashing behavior - crashes when any of the perl scripts crashes.
8) Input format integrity testing - not allowing any of the files to go to next steps if they are not of proper format
9) Deleting files when they are not any more needed (currently saves all files from FLASHing step onwards)

10) Organising output folders for easy input to FourCSeq, PeakC, r3Cseq (possibly generating pre-input files for these in output)
11) Keeping track who is running and if the run crashed