jacob-ogre

tl; dr: If parallelizing NUCmer by dividing a query into pieces, use the --prefix
flag to ensure separate mgap files are created rather than the single out.mgap.

### Fuller explanation ###
Trying to parallelize NUCmer alignment of assembly contigs to PacBio reads I ran
(repeatedly) into the error:

    ERROR: Could not parse input from 'Query File'.
    Please check the filename and format, or file a bug report

jacob-ogre

[
	{
		"args": null,
		"command": "enter_visual_mode"
	},
	{
		"args":
		{
			"action_args": null,
			"action_command": null,

jacob-ogre

[
    // Working in some additional Vim or Vim-like bindings; using 'g' as <leader>
    // because it's homerow and unused for most commands:
    { "keys": ["g", "t"], "command": "next_view", "context": [{"key": "setting.command_mode"}] },
    { "keys": ["g", "r"], "command": "prev_view", "context": [{"key": "setting.command_mode"}] },
    { "keys": ["g", "n"], "command": "focus_side_bar", "context": [{"key": "setting.command_mode"}] },
    { "keys": ["g", "w"], "command": "focus_group", "args": { "group": 0 } },
    { "keys": ["g", "m"], "command": "find_under_expand", "context": [{"key": "setting.command_mode"}] },
    { "keys": ["g", "s"], "command": "sftp_browse_server", "context": [{"key": "setting.command_mode"}] },

jacob-ogre

function tab_ncol {
    awk 'BEGIN {FS="\t"} ; END{print NF}' $1;
}
alias tncol='tab_ncol' 

function comma_ncol {
    awk 'BEGIN {FS=","} ; END{print NF}' $1;
}
alias cncol='comma_ncol' 

jacob-ogre

<snippet>
    <content><![CDATA[
with open(${1:fil}, 'wb') as ${2:out}:
    ${3:code}
]]></content>
    <tabTrigger>write</tabTrigger>
    <scope>source.python</scope>
    <description>WithOpenOut</description>
</snippet>

jacob-ogre

<snippet>
    <content><![CDATA[
"""${1:One-liner docstring}"""]]></content>
    <tabTrigger>docs</tabTrigger>
    <scope>source.python</scope>
    <description>Short Docstring</description>
</snippet>

jacob-ogre

<snippet>
    <content><![CDATA[
"""
${1:One-liner}

USAGE:
    python ${2:file} ${3:args...}
ARGS:
    ${4:arg, explanation}
RETURNS:

jacob-ogre

import sublime, sublime_plugin

class NerdTreeCloseCommand(sublime_plugin.WindowCommand):
    def run(self):
        self.window.run_command("focus_group", {"group": 0} )
        self.window.run_command("toggle_side_bar")

jacob-ogre

import sublime, sublime_plugin

class NerdTreeCommand(sublime_plugin.WindowCommand):
    def run(self):
        self.window.run_command("toggle_side_bar")
        self.window.run_command("focus_side_bar")

jacob-ogre

new
split-window -h -p 50 -t 0
split-window -v -p 30 -t 1
 
# pane number display
set-window-option -g window-status-current-bg yellow

# keybindings
set-window-option -g mode-keys vi