refined bases mask
adding new flow for future implementation of bcl2fastq
added not in use message
added another note about new flow
Merge branch 'develop' into illWork
registration of only relevant paired end data when paired end is run where not requested.
moved confirmCellLibrariesAssociatedWithBamFiles() from sampleService to mps.sequencingService; while the method worked well in sampleService, it appears to have prevented wasp-file from starting up its server, as it did not know bamFileType. Let's see what happens now.
removed escapeXml=false on comments and jobSubmit.comments, as well as the StringEscapeUtils.escapeXml in jobSubmissionController.comments; appears to behave fine
* Fix cross domain resource request for PDF viewing
* Implement Ext js style PDF viewer panel
* Same as previous, some modified files missing from commit
* Minor fix for the incl path of pdf.js lib in treeview.js.jsp
fixed stupid bug
if multiple work units write to same output folder they were competing for writing PROCESSING_INCOMPLETE_FILENAME. Now prefix with workunit id
added functionality to add a controlLibrary without any adaptor/barcode using loading via xml. Reviewed and reworked addControlToFlowCell functionality to deal with library w/o index. Changed flow to permit only a single control per lane. Reworked addLibraryToFlowCell (not a control) to deal with any library lacking a barcode - can have ONE library w/o barcode per lane, be it controlLibrary or job-related library. Can have one job-related library lacking barcode in addition to other libraries that have barcodes. A barcode must appear only once (even if it's no barcode). Reworked removal of conrol/job-related library from flow cell to display the WAIT message to prevent double button clicks; did same on the home/samples page for some step (it made sense). Modified a test in TestSampleSerivceImp to pass due to change in getLibrariesOnCell(cell).
moved
Merge branch 'develop' into qcChipSeqFlow
fixed blocking in proc.waitFor() caused by not consuming streams
trivial fix
Merge branch 'develop' of http://frankfurt.aecom.yu.edu/git/wasp/rob into develop
bug in read mask