Robert Hubley
Robert Hubley
## Problem description gt ltrharvest can hang in a rpc_wait_bit_killable state indefinitely under certain circumstances without any obvious timeout-to-failure. ## Exact command line call triggering the problem ``` % cd...
hi, shell likes: RepeatMasker-open-4-0-9/RepeatMasker/RepeatProteinMask -noLowSimple -pvalue 0.0001 *.fasta it cost more than 521.6h ,Neither repeatmasker nor repeatmodel are suited to deal with large genomes，they often runs for nearly 20 days...
MSP
Are there any plans to implement a multiple high scoring pairs ( MSP ) version of your algorithms? Perhaps its there and I don't see the options to invoke it....
I haven't been able to get a simple DNA search to produce a result. I am sure I am doing something silly. I couldn't find a simple invocation example for...
In the WFALM library there is an API that produces a seeded local alignment ( ends-free extension ) specified using two anchor points: ``` aligner_sw.wavefront_align_local_low_mem(local_seq1.c_str(), local_seq1.size(), local_seq2.c_str(), local_seq2.size(), anchor_begin_1, anchor_end_1,...
This would be a really useful enhancement. Currently it appears to ignore the -M flag when used with "-p 0".
I have a naive question about your MSA methodology. Why would the aligner choose to align short segments (1000bp) before aligning again? Perhaps I am misunderstanding the parameters to abPOA....
Obtaining the 1.5.1 files via the tar'd release: ``` wget https://github.com/yangao07/abPOA/releases/download/v1.5.1/abPOA-v1.5.1.tar.gz ``` Doesn't appear to have the -a option. Although it's in current main branch of the repository.
Feature Request: While I understand the necessity for ID conversion, the way it's implemented breaks downstream processing of the results. There are two ways to solve this (that I can...
I am wondering if you have thought about ways you might allow for shorter segment lengths (