Adam English

FASTA/Q name space handling

Thanks Related: https://sourceforge.net/p/pb-jelly/tickets/7/

Clean UI

I can't help you estimate how long it'll take. Hopefully it's done by now? Related: https://sourceforge.net/p/pb-jelly/tickets/6/

better progress tracking

--minIndelErr, and insertion/deletion in the alignment needs to be over -m basepairs before we consider it for potential SV evaluation. This helps get rid of most of the sequencing errors since pacbio reads' main mistakes are single base pair insertions or deletions. --threshold, is the minimum number of reads needed to support a varaint before it's considered for SV evaluation --spanMax, if there's a region longer than this threshold where we have a signal of an SV, we ignore it. This helps filter...

Not all reads are mapped in an orientation that allows them to confidently span the region of interest. Additionally, sometimes, alignment of the long-noisy reads using blasr can 'hide' the variant (e.g. supurious matches to bases that have been deleted in order to gain a better alignment score). Alternate supporting reads those supporting the variant and are fed into the assembly process for refinement. Reference reads are those that confidently span the region of interest.

Hello Urmi, Could you also look in the folder for the assembly/ ref0004924.2e3_ref0004924.3e5 and see what's there? Should maybe be some logs or sequence files or jsons. Something about that particular assembly is breaking the pipeline. On Tue, May 16, 2017 at 1:46 AM, Urmi Trivedi urmi208@users.sf.net wrote: Hello Chris and Adam, I am facing same error. 2017-05-09 11:18:44,904 [DEBUG] Getting fill sequence for ref0004924.2e3_ref0004924.3e5 2017-05-09 11:18:44,904 [DEBUG] No predicted gap size Traceback...