--- a/XCompose Wed Dec 10 11:07:06 2025 -0500
+++ b/XCompose Thu Jan 29 13:29:06 2026 -0500
@@ -100,4 +100,3 @@
-
--- a/bash_profile Wed Dec 10 11:07:06 2025 -0500
+++ b/bash_profile Thu Jan 29 13:29:06 2026 -0500
@@ -106,7 +106,7 @@
export LESS_TERMCAP_md=$(printf '\e[01;38;5;74m') # begin bold
export LESS_TERMCAP_me=$(printf '\e[0m') # end mode
export LESS_TERMCAP_se=$(printf '\e[0m') # end standout-mode
-export LESS_TERMCAP_so=$(printf '\e[38;5;246m') # begin standout-mode - info box
+export LESS_TERMCAP_so=$(printf '\e[38;5;16m\e[48;5;11m') # begin standout-mode - info box
export LESS_TERMCAP_ue=$(printf '\e[0m') # end underline
export LESS_TERMCAP_us=$(printf '\e[04;38;5;146m') # begin underline
export PAGER='less -iX'
--- a/fish/config.fish Wed Dec 10 11:07:06 2025 -0500
+++ b/fish/config.fish Thu Jan 29 13:29:06 2026 -0500
@@ -141,8 +141,8 @@
set -g -x LESS_TERMCAP_mb (printf '\e[01;31m') # begin blinking
set -g -x LESS_TERMCAP_md (printf '\e[01;38;5;74m') # begin bold
set -g -x LESS_TERMCAP_me (printf '\e[0m') # end mode
+set -g -x LESS_TERMCAP_so (printf '\e[38;5;16m\e[48;5;11m') # begin standout-mode - info box
set -g -x LESS_TERMCAP_se (printf '\e[0m') # end standout-mode
-set -g -x LESS_TERMCAP_so (printf '\e[38;5;246m') # begin standout-mode - info box
set -g -x LESS_TERMCAP_ue (printf '\e[0m') # end underline
set -g -x LESS_TERMCAP_us (printf '\e[04;38;5;146m') # begin underline
--- a/remote/bash_profile Wed Dec 10 11:07:06 2025 -0500
+++ b/remote/bash_profile Thu Jan 29 13:29:06 2026 -0500
@@ -99,7 +99,7 @@
export LESS_TERMCAP_md=$(printf '\e[01;38;5;74m') # begin bold
export LESS_TERMCAP_me=$(printf '\e[0m') # end mode
export LESS_TERMCAP_se=$(printf '\e[0m') # end standout-mode
-export LESS_TERMCAP_so=$(printf '\e[38;5;246m') # begin standout-mode - info box
+export LESS_TERMCAP_so=$(printf '\e[38;5;16m\e[48;5;11m') # begin standout-mode - info box
export LESS_TERMCAP_ue=$(printf '\e[0m') # end underline
export LESS_TERMCAP_us=$(printf '\e[04;38;5;146m') # begin underline
export PAGER='less -iX'
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/remote/bin/fastq-grep Thu Jan 29 13:29:06 2026 -0500
@@ -0,0 +1,1 @@
+../../bin/fastq-grep
\ No newline at end of file
--- a/stumpwm/external-screens.lisp Wed Dec 10 11:07:06 2025 -0500
+++ b/stumpwm/external-screens.lisp Thu Jan 29 13:29:06 2026 -0500
@@ -1,5 +1,87 @@
(in-package :stumpwm-user)
+(defun parse-xrandr-display-line (line)
+ (str:words (str:replace-all " +[(]normal.+[)].*" "" line :regex t)
+ :limit 2))
+
+(defun xrandr% ()
+ (reverse
+ (iterate
+ (with modes = (list))
+ ;; reverse to avoid final extra collect
+ (for line :in (reverse (sh '("xrandr") :result-type 'list)))
+ (when (str:starts-with-p "Screen " line)
+ (next-iteration))
+ (if (str:starts-with-p " " line)
+ (push (str:trim line) modes)
+ (progn (collect (list (parse-xrandr-display-line line) modes))
+ (setf modes nil))))))
+
+
+(defun xrandr/auto (display)
+ (sh `("xrandr" "--output" ,display "--auto") :wait nil))
+
+(defun xrandr/primary (display)
+ (sh `("xrandr" "--output" ,display "--primary") :wait nil))
+
+(defun xrandr/off (display)
+ (sh `("xrandr" "--output" ,display "--off") :wait nil))
+
+(defun xrandr/mode (display mode)
+ (sh `("xrandr" "--output" ,display "--mode" ,mode) :wait nil))
+
+(defun xrandr/dir (display dir other-display)
+ (sh `("xrandr" "--output" ,display
+ ,(ecase dir
+ (:left "--left-of")
+ (:right "--right-of")
+ (:same-as "--same-as"))
+ ,other-display)
+ :wait nil))
+
+(defun xrandr/menu-display (&aux (entries (xrandr%)))
+ (second (select-from-menu
+ (current-screen)
+ (mapcar (lambda (entry)
+ (destructuring-bind ((display state) modes) entry
+ (list (format nil "~A (~D modes) ~A"
+ display (length modes) state)
+ entry)))
+ entries)
+ "xrandr display:")))
+
+(defun xrandr/menu-action (entry)
+ (destructuring-bind ((display state) modes) entry
+ (declare (ignore state))
+ (second (select-from-menu
+ (current-screen)
+ (list* '("auto" :auto)
+ '("primary" :primary)
+ '("off" :off)
+ '("left of" :left)
+ '("right of" :right)
+ '("same as" :same-as)
+ (loop :for mode in modes
+ :collect (list mode (first (str:words mode)))))
+ (format nil "xrandr / ~A:" display)))))
+
+(defcommand xrandr () ()
+ (when-let ((display-entry (xrandr/menu-display)))
+ (destructuring-bind ((display state) modes) display-entry
+ (declare (ignore state modes))
+ (when-let ((action (xrandr/menu-action display-entry)))
+ (cond
+ ((eql action :off) (xrandr/off display))
+ ((eql action :auto) (xrandr/auto display))
+ ((eql action :primary) (xrandr/primary display))
+ ((member action '(:left :right :same-as))
+ (when-let ((other-display-entry (xrandr/menu-display)))
+ (destructuring-bind ((other-display state) modes) other-display-entry
+ (declare (ignore state modes))
+ (xrandr/dir display action other-display))))
+ (t (xrandr/mode display action)))))))
+
+
(defcommand screen-laptop () ()
(only)
(hostcase
--- a/stumpwm/igv.lisp Wed Dec 10 11:07:06 2025 -0500
+++ b/stumpwm/igv.lisp Thu Jan 29 13:29:06 2026 -0500
@@ -84,10 +84,12 @@
(group% :selected))
(defcommand igv/clear-read-selections () ()
- (clear-read-selections%))
+ (clear-read-selections%)
+ (group% nil))
(defcommand igv/select-reads () ()
(select-reads%)
+ (sleep 0.1)
(group% :selected))
(defcommand igv/goto () ()
@@ -104,8 +106,12 @@
(defcommand igv/goto-read () ()
(clear-read-selections%)
- (goto%)
- (select-reads%))
+ (sleep 0.1)
+ (select-reads%)
+ (sleep 0.1)
+ (group% :selected)
+ (sleep 0.1)
+ (goto%))
(defcommand igv/init () ()
(send-igv-batch-file "/home/sjl/bin/igv.batch"))
--- a/stumpwm/key-mapping.lisp Wed Dec 10 11:07:06 2025 -0500
+++ b/stumpwm/key-mapping.lisp Thu Jan 29 13:29:06 2026 -0500
@@ -30,8 +30,6 @@
("H-SunPageDown" "st-font-down")
("H-z" "fullscreen")
("H-Z" "end-zoom")
- ("S-H-F1" "bht")
- ("C-S-F1" "bht")
("H-F4" "switch-yubikeys")
("H-\\" "pass-personal")
("H-|" "generate-password")
@@ -83,16 +81,6 @@
("H-8" "gselect 8")
("H-9" "gselect 9")
- ("KP_Insert" "vgroups")
- ("KP_End" "gselect 1")
- ("KP_Down" "gselect 2")
- ("KP_Page_Down" "gselect 3")
- ("KP_Left" "gselect 4")
- ("KP_Begin" "gselect 5")
- ("KP_Right" "gselect 6")
- ("KP_Home" "gselect 7")
- ("KP_Up" "gselect 8")
- ("KP_Page_Up" "gselect 9")
("H-!" "gmove 1")
("H-@" "gmove 2")
@@ -152,7 +140,8 @@
("H-F5" "rotate-brightness-down")
("H-F6" "rotate-brightness-up")
("H-F7" "screen-laptop")
- ("H-F8" "screen-external"))
+ ("H-F8" "screen-external")
+ ("H-x" "xrandr"))
(define-top-keys ;; layout
("s-H-o" "only")
@@ -184,6 +173,20 @@
("H-F11" "toggle-current-mode-line")
("H-F12" "refresh-heads"))
+(define-top-keys ;; sinc numpad
+ ("KP_Insert" "vgroups")
+ ("KP_End" "gselect 1") ; 1
+ ("KP_Down" "gselect 2") ; 2
+ ("KP_Page_Down" "gselect 3") ; 3
+ ("KP_Left" "gselect 4") ; 4
+
+ ("KP_Begin" "gselect 5") ; 5
+ ("KP_Right" "gselect 6") ; 6
+ ("KP_Home" "igv/minimera") ; 7
+ ("KP_Up" "igv/clear-read-selections") ; 8
+ ("KP_Page_Up" "igv/select-reads") ; 9
+ )
+
(defvar *keymap/igv* (make-sparse-keymap))
(define-key *keymap/igv* (kbd "s") "igv/supplementary-on")
@@ -247,7 +250,8 @@
)
(define-top-keys ;; Single-key keyboard
- ("S-C-F1" "igv"))
+ ("S-C-F1" "bht")
+ ("S-H-F1" "bht"))
(define-remapped-keys
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/stumpwm/local-share-stumpwm/3440/thirds.dump Thu Jan 29 13:29:06 2026 -0500
@@ -0,0 +1,1 @@
+../um-dev.dump
\ No newline at end of file
--- a/stumpwm/package.lisp Wed Dec 10 11:07:06 2025 -0500
+++ b/stumpwm/package.lisp Thu Jan 29 13:29:06 2026 -0500
@@ -1,5 +1,7 @@
(in-package :stumpwm-user)
(shadow :window)
+(shadow :next)
(use-package :losh)
+(use-package :iterate)
--- a/stumpwm/stumpconfig.asd Wed Dec 10 11:07:06 2025 -0500
+++ b/stumpwm/stumpconfig.asd Thu Jan 29 13:29:06 2026 -0500
@@ -9,6 +9,7 @@
:jarl
:local-time
:losh
+ :iterate
:parse-number
:split-sequence
:str
--- a/stumpwm/terminal-fonts.lisp Wed Dec 10 11:07:06 2025 -0500
+++ b/stumpwm/terminal-fonts.lisp Thu Jan 29 13:29:06 2026 -0500
@@ -33,4 +33,8 @@
((:integer "Size: "))
(setf *terminal-font-size* size))
+(defcommand terminal-font-size-set (size)
+ ((:integer "Size: "))
+ (setf *terminal-font-size* size))
+
--- a/vim/vimrc-minimal Wed Dec 10 11:07:06 2025 -0500
+++ b/vim/vimrc-minimal Thu Jan 29 13:29:06 2026 -0500
@@ -30,9 +30,9 @@
set undoreload=10000
set list
set listchars=tab:▸\ ,eol:¬,extends:❯,precedes:❮
+set showbreak=↪
set lazyredraw
set matchtime=3
-set showbreak=↪
set splitbelow
set splitright
set autowrite