cmdcolin

Text-editor saturday

My text editor avante.nvim is just going crazy. Previously it dumped diffs into the 'chat sidebar', and I'd accept them with "A" in the sidebar then accept all with "ca" in the main area...vibe coding. But the avante.nvim switched to running tools that run the edits instead, and is just going crazy with tool usage despite me having disable_tools enabled. I dunno. Maybe I should file a bug. But this spurred me to try to work holistically on my editing skills this morning. I just looked at my config and tweaked a million things...

Trying out rose-pine

Trying rose-pine color scheme. It is kinda funny with tons of italic but it's cute

cmdcolin

import fs from 'fs'

const tracks = JSON.parse(fs.readFileSync(process.argv[2], 'utf8')) as {
  tracks: any[]
}

const asm = 'B73'
const assemblyNames = [asm]
const base = 'https://jbrowse.maizegdb.org/B73/'
console.log(

cmdcolin

[
  { "role": "user", "type": "message", "content": "hello" },
  {
    "role": "assistant",
    "type": "message",
    "content": "Hello! How can I help you today?\n"
  },
  {
    "role": "user",
    "type": "message",

cmdcolin

cmdcolin

#!/bin/bash

# create a bed file from hap-ibd output with columns "chr, start, end, sample_name1 hap1 sample_name2 hap2"
# add this config to jbrowse get(feature,'sample1')+':HP'+get(feature,'hap1')+'     '+get(feature,'sample2')+':HP'+get(feature,'hap2')

# Process file in a fully streaming fashion and pipe directly to bgzip
# Combine header and data in a single stream
(
  echo -e "#chr\tstart\tend\tsample1\thap1\tsample2\thap2"
  zcat "$1" | awk -F'\t' '{print $5"\t"$6"\t"$7"\t"$1"\t"$2"\t"$3"\t"$4}'

cmdcolin

Fixing Disk Usage Analyzer (aka baobab) bug where it was deleting the wrong file

Issue thread https://gitlab.gnome.org/GNOME/baobab/-/issues/157#note_2367208

Background on the bug

The Disk Usage Analyzer app (aka baobab) has a "bug" where if you right-click a file, it brings up a context menu and you can then click "Move to Trash". However, if your mouse moves outside the context menu, then it "highlights" or "selects" a different file with the context menu still open, and then trashes the newly highlighted/selected file instead of the one that you originally right-clicked

cmdcolin

If you want to publish ESM/CJS you can update your package.json to use the
"exports" field, and run the tsc compiler twice over the code, once using
--module cjs

```json
{
  "name": "dualpackage",
  "version": "1.0.0",
  "description": "demo of dual esm/cjs package",

cmdcolin

One thing that is important to note about JBrowse is that it is a "static site compatible application"

What is a "static site"?

A static site is just a set of plain files like HTML, JS, and CSS

Static sites don't use dynamic "server side" code like PHP, Node.js, Java Servlets, or things like that.

cmdcolin

import eslint from '@eslint/js'
import importPlugin from 'eslint-plugin-import'
import eslintPluginReact from 'eslint-plugin-react'
import eslintPluginReactHooks from 'eslint-plugin-react-hooks'
import tseslint from 'typescript-eslint'

export default tseslint.config(
  {
    // might be able to find a way to not ignore some of these but i just ignore them
    ignores: [

cmdcolin

JBrowse 2 has a special "view type" called the "breakpoint split view" that allows you to see the connection between split long reads (e.g. SA tag) and paired-end reads

Ways to access the breakpoint split view

Using the SV inspector to launch a breakpoint split view

The SV inspector lets you load a VCF containing SV calls and then will launch a "breakpoint split view". Note that the breakpoint split view that it launches will be empty but you can then add your BAM or CRAM reads to it (on both top and bottom levels sometimes is needed)