Jeremy Jay

Show/confirm dependency tree

1

Looks like the parser might need more complexity for this, but just wanted to throw out a vote for displaying a build dependency tree. I use make for a number...

Needs some backtracking in `makeFormatter`, currently "dddd" becomes "Sunday" but then "d" is applied to become "Sun11ay"

integer divide by zero using the -U option

4

Looks like there is some progress using the -U option (I no longer get "uniprot error: 400 Bad request"), but I now see the following after entering the Uniprot ID...

uniprot changed data format

1

The `-uniprot` option is broken since Uniprot changed their data interchange format: https://web.expasy.org/docs/userman.html#FT_line The current code was based on the format which was current as of March 2019: http://web.archive.org/web/20190213124909/https://web.expasy.org/docs/userman.html#FT_line

Consensus misses last base

3

I believe the "sentinal" tag at [falcon.c:157](https://github.com/PacificBiosciences/FALCON/blob/master/src/c/falcon.c#L157) should also record the previous information (p_j, p_jj, p_q_base). Otherwise the g_best_ck used on line 494 refers to the previous-to-the-last base and the...

Probably works but untested - may need another supporting change to get_cns_from_align_tags

View template should support type-specific templates

5

The current specification requires the view template to only have an `{{id}}` placeholder. However, for services that support multiple types, the view template could be substantially different for each type....

can’t be opened because Apple cannot check it for malicious software

1

MacOS gives an error when trying to run the latest releases: ``` “lollipops” can’t be opened because Apple cannot check it for malicious software. ``` ![Screenshot 2023-10-05 at 1 04...

It would be useful to get notifications when long-running code uses too much memory. Then it could dynamically tune parallelism to ensure it doesn't overcommit. Something similar to this interface...