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Below the out-dated (incomplete) list of fixes, upto 16Nov2017

Updated by Jelena - 17:30 16/Nov/2017

CB4 - CCseqBasic4 ("First stable portable CC4") - launched 10/Jan/2017

Bug fixes and updates (after release) :

16/Nov/2017 Rollback update - Rolled back to last stable release : CB4a is now "outdated" and returned to its latest stable form.

These updates were there only temporarily :

01/Nov/2017 Added feature - Added "tentative" UMI indexing support. All questions about this developmental feature to Damien Downes !

01/Nov/2017 Bug fix - The Bowtie2 support (01Oct2017 below) was crashing as config files weren't found. Now fixed.

01/Nov/2017 Bug fix - Bowtie2 run TRIMMING and FLASHING has all been ran in PHRED64 even if the data was PHRED33. Now fixed.

02/Oct/2017 Added feature - Added Bowtie2 support . Use with flag --bowtie2 . Report all problems to Jelena !

These fixes are part of the stable release :

08/Nov/2017 Portability improvement - Adding support to "all tools already in path" run mode

08/Nov/2017 Bug fix - Server path and server type weren't portable yet. Now fixed.

01/Nov/2017 Bug fix - qmin parameter (--qualFilter from 25/Jan/2017 below) didn't go through properly. Now fixed.

01/Nov/2017 Bug fix - Bowtie1 run TRIMMING and FLASHING has all been ran in PHRED33 even if the data was PHRED64. Now fixed.

31/Oct/2017 Bug fix Portability fix 27/10 below had a typo in file paths (not all were changed to portable ones - so blat filtering crashed). Now fixed.

27/Oct/2017 Portability improvement - Divided configuration file to 3 parts, added testEnvironment.sh for setting up the tool easily

08/Sep/2017 Portability fix Detached the intersectappend.pl from CBRG system - to use within-CCsewBasic copy of intersectappend code instead (for portability).

07/Sep/2017 Bug fix Bowtie parameter -M was broken (caused error). Now fixed.

07/Sep/2017 Portability fix Removed last hard-coded path $bigwig_folder from analyseMappedReads.pl

06/Sep/2017 Bug fix Cis and trans reporter counters (and marks in bam files) : some cis reads were counted as trans reads. Now fixed.

01/Sep/2017 Typo fix - Fixed the fasta configuration path for mm9PARP artificial construct support .

31/Aug/2017 Added feature - Added PARP artificial construct support to the pipe, to be asked with --genome mm9PARP .

23/Jun/2017 Added feature - Added cis and trans counters for the reporters. Added short versions of report files for quick skim through of results.

25/May/2017 Added feature - Added informative exit message for situations where run crashes "just after BLAT" as it is ran with "test fastq" just to generate psl files for BLAT.

25/May/2017 Added feature - Added disk usage checkpoints for fastq combining and iterative mapping steps (to better catch situations where user runs out of quota during the run) .

24/Apr/2017 Bug fix Flag --BLATforREUSEfolderPath conducted "merged" oligo filtering for oligo names which contained each others. Now fixed.

25/Jan/2017 Portability fix Added flag --qualFilter 20 (to set trimming quality score treshold)

25/Jan/2017 Portability fix Possible to set custom names to otuput log and error files --outfile qsub.out --errfile qsub.err

25/Jan/2017 Portability fix Adding extra bowtie flags --seedlen --seedmms --maqerr

24/Jan/2017 Portability fix Flag name --saveDpnGenome to be --saveGenomeDigest

24/Jan/2017 Portability fix VersionInfo subroutine fix (now works)

24/Jan/2017 Portability fix Taking out all python and perl calls which used shebang (to avoid overwriting the set environment)

24/Jan/2017 Portability fix Not any more copying the perl scripts to run dir when running them (bad habit)

CB3 - CCseqBasic3 ("First stable portable CC3") - launched 10/Jan/2017

Bug fixes and updates (after release) :

16/Nov/2017 Rollback update - Rolled back to last stable release : CB4a is now "outdated" and returned to its latest stable form.

These updates were there only temporarily :

01/Nov/2017 Bug fix - The Bowtie2 support (01Oct2017 below) was crashing as config files weren't found. Now fixed.

01/Nov/2017 Bug fix - Bowtie2 run TRIMMING has all been ran in PHRED64 even if the data was PHRED33. Now fixed.

02/Oct/2017 Added feature - Added Bowtie2 support . Use with flag --bowtie2 . Report all problems to Jelena !

( plus all the fixes below )