--- a/bash_profile Thu May 23 13:50:23 2024 -0400
+++ b/bash_profile Wed Jun 12 14:42:07 2024 -0400
@@ -22,12 +22,12 @@
eval "$(dircolors -b ~/.dircolors)"
fi
-D=$'\e[37m'
-RED=$'\e[31m'
-GREEN=$'\e[32m'
-ORANGE=$'\e[33m'
-BLUE=$'\e[34m'
-PINK=$'\e[35m'
+D=$'\x01\e[37m\x02'
+RED=$'\x01\e[31m\x02'
+GREEN=$'\x01\e[32m\x02'
+ORANGE=$'\x01\e[33m\x02'
+BLUE=$'\x01\e[34m\x02'
+PINK=$'\x01\e[35m\x02'
# CYAN=$'\e[36m'
function last_return_value() {
@@ -47,7 +47,7 @@
HOST_COLOR="$ORANGE"
fi
-export PS1='\n\[${PINK}\]\u \[${D}\]at \[${HOST_COLOR}\]\h \[${D}\]in \[${GREEN}\]\w\[${D}\] $(last_return_value)$ '
+export PS1='\n${PINK}\u ${D}at ${HOST_COLOR}\h ${D}in ${GREEN}\w${D} $(last_return_value)$ '
alias ..="cd .."
alias ...="cd ../.."
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/sv Wed Jun 12 14:42:07 2024 -0400
@@ -0,0 +1,5 @@
+#!/usr/bin/env bash
+
+set -euo pipefail
+
+column -s ' ' -t "$@"
--- a/fish/functions/el.fish Thu May 23 13:50:23 2024 -0400
+++ b/fish/functions/el.fish Wed Jun 12 14:42:07 2024 -0400
@@ -1,8 +1,8 @@
function el -d "Edit lab notes"
pushd ~/lab
- hg pull -u
+ ./pull.sh
nvim README.markdown
hg ci -m 'Update'
- hg push
+ ./push.sh
popd
end
--- a/remote/bash_profile Thu May 23 13:50:23 2024 -0400
+++ b/remote/bash_profile Wed Jun 12 14:42:07 2024 -0400
@@ -24,12 +24,12 @@
eval "$(dircolors -b ~/.dircolors)"
fi
-D=$'\e[37m'
-RED=$'\e[31m'
-GREEN=$'\e[32m'
-ORANGE=$'\e[33m'
-BLUE=$'\e[34m'
-PINK=$'\e[35m'
+D=$'\x01\e[37m\x02'
+RED=$'\x01\e[31m\x02'
+GREEN=$'\x01\e[32m\x02'
+ORANGE=$'\x01\e[33m\x02'
+BLUE=$'\x01\e[34m\x02'
+PINK=$'\x01\e[35m\x02'
# CYAN=$'\e[36m'
function last_return_value() {
@@ -53,7 +53,7 @@
HOST_COLOR="$ORANGE"
fi
-export PS1='\n\[${PINK}\]\u \[${D}\]at \[${HOST_COLOR}\]\h \[${D}\]in \[${GREEN}\]\w\[${D}\] $(last_return_value)$ '
+export PS1='\n${PINK}\u ${D}at ${HOST_COLOR}\h ${D}in ${GREEN}\w${D} $(last_return_value)$ '
alias ..="cd .."
alias ...="cd ../.."
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/remote/bin/fnums Wed Jun 12 14:42:07 2024 -0400
@@ -0,0 +1,1 @@
+../../bin/fnums
\ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/remote/bin/sv Wed Jun 12 14:42:07 2024 -0400
@@ -0,0 +1,1 @@
+../../bin/sv
\ No newline at end of file
--- a/stumpwm/icelandic.lisp Thu May 23 13:50:23 2024 -0400
+++ b/stumpwm/icelandic.lisp Wed Jun 12 14:42:07 2024 -0400
@@ -1,21 +1,5 @@
(in-package :stumpwm-user)
-(defcommand send-key (key &optional (win (current-window))) (:key)
- "Send key press and key release events for KEY to window WIN."
- ;; from https://github.com/alezost/stumpwm-config/blob/master/utils.lisp
- (let ((xwin (window-xwin win)))
- (multiple-value-bind (code state) (stumpwm::key-to-keycode+state key)
- (flet ((send (event)
- (xlib:send-event xwin event (xlib:make-event-mask event)
- :display *display*
- :root (screen-root (window-screen win))
- :x 0 :y 0 :root-x 0 :root-y 0
- :window xwin :event-window xwin
- :code code
- :state state)))
- (send :key-press)
- (send :key-release)
- (xlib:display-finish-output *display*)))))
(defun send-keys (keys &key (win (current-window)) (sleep 0))
(dolist (k keys)
--- a/stumpwm/key-mapping.lisp Thu May 23 13:50:23 2024 -0400
+++ b/stumpwm/key-mapping.lisp Wed Jun 12 14:42:07 2024 -0400
@@ -159,6 +159,13 @@
("H-F11" "toggle-current-mode-line")
("H-F12" "refresh-heads"))
+(defvar *keymap/igv* (make-sparse-keymap))
+
+(define-key *keymap/igv* (kbd "s") "igv/toggle-supplementary-alignments")
+
+(define-top-keys ;; alternate maps
+ ("H-i" *keymap/igv*))
+
;;; The G A M E R M O U S E:
;;;
--- a/stumpwm/miscellaneous.lisp Thu May 23 13:50:23 2024 -0400
+++ b/stumpwm/miscellaneous.lisp Wed Jun 12 14:42:07 2024 -0400
@@ -79,3 +79,20 @@
(echo "Starting VM.")
(run-shell-command "/home/sjl/vms/run"))
+
+(defun send-igv-command (string)
+ (usocket:with-client-socket (socket stream "127.0.0.1" 60151)
+ (unwind-protect (progn (write-line string stream)
+ (force-output stream))
+ (usocket:socket-close socket))))
+
+(defvar *igv/supplementary-alignments* t)
+
+(defcommand igv/toggle-supplementary-alignments () ()
+ (callf *igv/supplementary-alignments* #'not)
+ (send-igv-command
+ (format nil "preference SAM.FILTER_SUPPLEMENTARY_ALIGNMENTS ~A"
+ (if *igv/supplementary-alignments* "FALSE" "TRUE")))
+ (echo (if *igv/supplementary-alignments*
+ "Supplementary alignments now on."
+ "Supplementary alignments now off.")))
--- a/stumpwm/stumpconfig.asd Thu May 23 13:50:23 2024 -0400
+++ b/stumpwm/stumpconfig.asd Wed Jun 12 14:42:07 2024 -0400
@@ -10,7 +10,8 @@
:cl-ppcre
:bordeaux-threads
:jarl
- :local-time)
+ :local-time
+ :usocket)
:serial t
:components ((:file "package")
--- a/stumpwm/utils.lisp Thu May 23 13:50:23 2024 -0400
+++ b/stumpwm/utils.lisp Wed Jun 12 14:42:07 2024 -0400
@@ -1,5 +1,27 @@
(in-package :stumpwm-user)
+(defun send-key% (key &optional (win (current-window)))
+ "Send key press and key release events for KEY to window WIN."
+ ;; from https://github.com/alezost/stumpwm-config/blob/master/utils.lisp
+ (let ((xwin (window-xwin win)))
+ (multiple-value-bind (code state) (stumpwm::key-to-keycode+state key)
+ (flet ((send (event)
+ (xlib:send-event xwin event (xlib:make-event-mask event)
+ :display *display*
+ :root (screen-root (window-screen win))
+ :x 0 :y 0 :root-x 0 :root-y 0
+ :window xwin :event-window xwin
+ :code code
+ :state state)))
+ (send :key-press)
+ (send :key-release)
+ (xlib:display-finish-output *display*)))))
+
+(defcommand send-key (key &optional (win (current-window))) (:key)
+ "Send key press and key release events for KEY to window WIN."
+ (send-key% key win))
+
+
(defun string-contains (needle string)
(and (search needle string :test #'char=) t))
--- a/vim/custom-dictionary.utf-8.add Thu May 23 13:50:23 2024 -0400
+++ b/vim/custom-dictionary.utf-8.add Wed Jun 12 14:42:07 2024 -0400
@@ -463,3 +463,9 @@
Nanopal
Slurm
hardcode
+SDS
+dropwise
+vortexing
+segfaulting
+segfaulted
+IGV
--- a/vim/vimrc Thu May 23 13:50:23 2024 -0400
+++ b/vim/vimrc Wed Jun 12 14:42:07 2024 -0400
@@ -1486,6 +1486,8 @@
au FileType fish setlocal commentstring=#\ %s
au FileType gnuplot setlocal commentstring=#\ %s
au FileType cs setlocal commentstring=//\ %s
+ au FileType c setlocal commentstring=//\ %s
+ au FileType cpp setlocal commentstring=//\ %s
au FileType arduino setlocal commentstring=//\ %s
au FileType pandabt setlocal commentstring=//\ %s
au FileType nextflow setlocal commentstring=//\ %s
@@ -1604,7 +1606,7 @@
nnoremap <f6> :Neoformat<cr>
let g:neoformat_snakemake_snakefmt = {
- \ 'exe': '/home/sjl/virtualenvs/snakemake/bin/snakefmt',
+ \ 'exe': '/home/sjl/bin/venvs/tools/bin/snakefmt',
\ 'args': [],
\ 'replace': 1,
\ 'stdin': 0,