Zamin Iqbal

Results 180 comments of Zamin Iqbal

Fix known bugs in genotyping and look at confidence distribution

I just want to check the genotyping of longer alleles and then ok to close. All unit tests pass including with valgrind.

Fix known bugs in genotyping and look at confidence distribution

OK, so in two parts. **Why does a ./. call have a confidence?** When Cortex genotypes a bubble, you pass it a model. That model is diploid or haploid at...

Max memory must be at least 8 * Bloomfilter size in bytes

ping @leoisl

Max memory must be at least 8 * Bloomfilter size in bytes

We're transitioning to using COBS (https://github.com/iqbal-lab-org/cobs) which is faster and uses less disk - see https://arxiv.org/abs/1905.09624

Is `find_mean_covg' still appropriate in estimate parameters?

went through exactly this with auto-cleaning for cortex. very hard to make a robust solution given how widely data can vary

Logging performance of de novo variant discovery with racon

This RAM use is, IMO, acceptable for the moment - i wouldn't postpone the merge to reduce RAM

Data for the paper to test software

Hi there - apologies for this. For what it's worth this is a known and temporary issue - the EBI ftp is a mess at the moment and they are...

Racon as a library

Thanks so much for this!!

Issue while choosing the reference path for genotyping

1. yes, this is possible. Pandora needs to make a "global" choice, of a path from one end of the gene to the other. Sometimes the data is such that...

Issue while choosing the reference path for genotyping

Omg we have not replied to you! So sorry @AmayAgrawal , we will return to this after the Xmas vacation