# HG changeset patch
# User Steve Losh <steve@stevelosh.com>
# Date 1718217727 14400
# Node ID cf74bfa5845a2e6e7c9e4c4f956e3e0fc3d9c28e
# Parent  f77ee236cdf3b2eb18fb2a85d465c414e8983d4d
More

diff -r f77ee236cdf3 -r cf74bfa5845a bash_profile
--- 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 ../.."
diff -r f77ee236cdf3 -r cf74bfa5845a bin/sv
--- /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 "$@"
diff -r f77ee236cdf3 -r cf74bfa5845a fish/functions/el.fish
--- a/fish/functions/el.fish	Thu May 23 13:50:23 2024 -0400
+++ b/fish/functions/el.fish	Wed Jun 12 14:42:07 2024 -0400
@@ -1,8 +1,8 @@
 function el -d "Edit lab notes"
     pushd ~/lab
-    hg pull -u
+    ./pull.sh
     nvim README.markdown
     hg ci -m 'Update'
-    hg push
+    ./push.sh
     popd
 end
diff -r f77ee236cdf3 -r cf74bfa5845a remote/bash_profile
--- a/remote/bash_profile	Thu May 23 13:50:23 2024 -0400
+++ b/remote/bash_profile	Wed Jun 12 14:42:07 2024 -0400
@@ -24,12 +24,12 @@
     eval "$(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 ../.."
diff -r f77ee236cdf3 -r cf74bfa5845a remote/bin/fnums
--- /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
diff -r f77ee236cdf3 -r cf74bfa5845a remote/bin/sv
--- /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
diff -r f77ee236cdf3 -r cf74bfa5845a stumpwm/icelandic.lisp
--- 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)
diff -r f77ee236cdf3 -r cf74bfa5845a stumpwm/key-mapping.lisp
--- 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:
 ;;;
diff -r f77ee236cdf3 -r cf74bfa5845a stumpwm/miscellaneous.lisp
--- 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.")))
diff -r f77ee236cdf3 -r cf74bfa5845a stumpwm/stumpconfig.asd
--- 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")
diff -r f77ee236cdf3 -r cf74bfa5845a stumpwm/utils.lisp
--- 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))
 
diff -r f77ee236cdf3 -r cf74bfa5845a vim/custom-dictionary.utf-8.add
--- 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
diff -r f77ee236cdf3 -r cf74bfa5845a vim/vimrc
--- 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,