John St. John

The conditional thing wouldn't cause the issue. You are building the error profile based on reads that align so the resulting error rate shouldn't be any worse than the original...

Unfortunately I am not going to have time to debug this. However I have uploaded the previous version to the Downloads page for you to try as well.

Cool! So it's working now?

Hello, I haven't yet implemented the fix to get around the problem of the reads being sorted by chromosome on the output. Reads are random within chromosomes, but they are...

Ah, you would have to make a new model that supports longer reads as well, which means you need sequencing data probably aligned to PhiX from the instrument you want...

It has been about 4 years since I last touched this. I think there is a c program in one of the subdirectories you could use (after compiling with Make)....

Is the seg fault in my prog or santools? On Mon, Dec 21, 2015 at 12:43 PM Yifang Tan [email protected] wrote: > Thanks! > The program is located in cUtils...

Nope. You'll have to do GDB to find out which line the program is crashing on. Ever used gdb before? I am away from a computer for a few weeks...

Could be an issue with supporting different read lengths? I have not tested that extensively. Does your pre-merging script do any trimming, or just complete discarding? Also have you checked...

You definitely want to preserve matching. If SeqPrep doesn’t just error out when it finds mismatching reads, it may just attempt to keep matching them pairwise until it gets to...