Heng Li
Heng Li
Thanks for the evaluation. This is very comprehensive. @ruanjue and I would like to investigate why wtdbg2 didn't work well. We wonder if you have the "true" assembly (i.e. the...
The sequence at the end of the message is a simulated sequence from GRCh38. The true position is chr7:4124634-4126723. ngmlr-0.2.5 gives a split alignment. The longer alignment is correct with...
For example, it doesn't report an error for preset "splice:hd".
There have been several github issues related to the installation of samtools/htslib. This is mainly because samtools requires a few non-trivial dependencies for advanced features such as https/htsget and bzip2/xz...
Example: ``` ##fileformat=VCFv4.1 ##FORMAT= ##contig= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1 S2 S3 S4 11 101 . GCGT G,GCGA,GTGA,CCGT 199 PASS . GT 0/1 1/2 2/3...
Another discussion thread. It is probably too early to implement libraries now, but it would be good to start thinking about the topic. Currently, gfatools comes with [very preliminary APIs](https://github.com/lh3/gfatools/blob/master/gfa.h)...
Walk/W-lines are used to keep sequence walks through the graph. There are a few options: 1. Don't add W-lines as we already have Path/P-lines in GFA1. However, there are multiple...
**What is the SO term name and accession?** SNP (SO:0000694) **Describe what you would like to change.** Drop the frequency requirement and change the definition to > SNPs are single...
When patching gaps between two anchors, we sometimes need to align two sequences of vastly different lengths. Suppose we are aligning a 10bp sequence against a 100kb sequence. The active...
Sdust produces wrong output for the following sequence: ```txt >TEST_SEQ AAACCCTACGCACACAAACCTCCCTCACACAANCCCTACGCNCACAAACCTNCCTCACACAAACCCTACGCACACAAACCTCCCTCACACAAACCCTACGCACACAAA ``` The sequence length is 108bp, but the range is `52 116`.