Benedict Paten

abPOA user specifiable seeds

6

Hi @yangao07 , I've been experimenting a little with the seeding in abpoa and am wondering if it would be possible to add an option for users to provide alignment...

Related to: https://github.com/glennhickey/hal/issues/3 May resolve once issues are fixed on all submodules, but I think special flags needed to be added to make kyototycoon and cabinet to build, using the...

Runtime assessments/using EC2 to benchmark

2

To write this up we need to record runtimes for how long it takes (wall and processing time) to process a minion dataset, both for marginAlign and marginCaller. I think...

marginAlign should output alignment quality scores, like BAQ, using the posterior probs it calculates.

I'm doing some test runs - it would be much quicker to split up the input fastq files to speed up last/bwa

Courtesy of Tim Sackton: I ran into another issue with progressiveCactus where a job that is issued with too little memory to finish will lead to a loop of that...

When restarting a jobTree parameter changes to the script (like changing the batch system) do not have any effect, because such parameters are overwritten when reading the state of the...

Obviously - though consideration needs to be made of the command line binaries - this could possibly be managed via the python path, removing the command line binaries.