# HG changeset patch # User Steve Losh # Date 1782751856 14400 # Node ID 581345d6b360dc8240a5f2198c7e68580e5a7bab # Parent c0d31d738157ca0455a4ebc0a083642f0299734f More diff -r c0d31d738157 -r 581345d6b360 bin/# --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bin/# Mon Jun 29 12:50:56 2026 -0400 @@ -0,0 +1,2 @@ +#!/usr/bin/env bash +cat diff -r c0d31d738157 -r 581345d6b360 bin/qimgv-stdin --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bin/qimgv-stdin Mon Jun 29 12:50:56 2026 -0400 @@ -0,0 +1,7 @@ +#!/usr/bin/env bash + +set -euo pipefail + +cat > ~/scratch/qimgv-tmp +qimgv ~/scratch/qimgv-tmp +rm -f ~/scratch/qimgv-tmp diff -r c0d31d738157 -r 581345d6b360 bin/watch-latex --- a/bin/watch-latex Mon Mar 02 13:12:13 2026 -0500 +++ b/bin/watch-latex Mon Jun 29 12:50:56 2026 -0400 @@ -5,4 +5,4 @@ NAME="$1" shift -echo "$NAME".tex "$@" | peat "mklatex $NAME" +echo *.tex "$@" | peat "mklatex $NAME" diff -r c0d31d738157 -r 581345d6b360 bin/x --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bin/x Mon Jun 29 12:50:56 2026 -0400 @@ -0,0 +1,1 @@ +scratch \ No newline at end of file diff -r c0d31d738157 -r 581345d6b360 fish/config.fish --- a/fish/config.fish Mon Mar 02 13:12:13 2026 -0500 +++ b/fish/config.fish Mon Jun 29 12:50:56 2026 -0400 @@ -149,7 +149,7 @@ set -g -x ANSIBLE_NOCOWS 1 set -g -x DFT_COLOR 'always' # disable stupid pipe detection -set -g -x DFT_WIDTH 10000000000 # stop trying to be smart +# set -g -x DFT_WIDTH 10000000000 # stop trying to be smart set -g -x DFT_TAB_WIDTH 8 # tabs are 8 characters wide set -g -x DFT_DISPLAY side-by-side set -g -x DFT_CONTEXT 8 # more context diff -r c0d31d738157 -r 581345d6b360 gitignore --- a/gitignore Mon Mar 02 13:12:13 2026 -0500 +++ b/gitignore Mon Jun 29 12:50:56 2026 -0400 @@ -21,5 +21,6 @@ sjl-*-push.sh sjl-*-pull.sh *.sif +Rplots.pdf *.waiting diff -r c0d31d738157 -r 581345d6b360 htoprc --- a/htoprc Mon Mar 02 13:12:13 2026 -0500 +++ b/htoprc Mon Jun 29 12:50:56 2026 -0400 @@ -38,7 +38,7 @@ column_meter_modes_0=1 1 1 column_meters_1=RightCPUs2 Tasks LoadAverage Uptime column_meter_modes_1=1 2 2 2 -tree_view=0 +tree_view=1 sort_key=39 tree_sort_key=0 sort_direction=-1 @@ -48,7 +48,7 @@ screen:Main=PID USER PRIORITY NICE M_RESIDENT STATE PERCENT_CPU PERCENT_MEM TIME Command .sort_key=M_RESIDENT .tree_sort_key=PID -.tree_view=0 +.tree_view=1 .tree_view_always_by_pid=1 .sort_direction=-1 .tree_sort_direction=1 diff -r c0d31d738157 -r 581345d6b360 lispwords --- a/lispwords Mon Mar 02 13:12:13 2026 -0500 +++ b/lispwords Mon Jun 29 12:50:56 2026 -0400 @@ -132,6 +132,7 @@ (2 define-interface) (1 make-option make-boolean-options make-group) (1 quit-on-ctrl-c) +(1 print-help-and-exit) ; metabang-bind diff -r c0d31d738157 -r 581345d6b360 stumpwm/bioinf.lisp --- a/stumpwm/bioinf.lisp Mon Mar 02 13:12:13 2026 -0500 +++ b/stumpwm/bioinf.lisp Mon Jun 29 12:50:56 2026 -0400 @@ -1,7 +1,10 @@ (in-package :stumpwm-user) -(defun random-base () +(defun random-rna-base () + (random-elt "GCAU")) + +(defun random-dna-base () (random-elt "GCAT")) (defun random-phred () @@ -13,21 +16,42 @@ (setf (char result i) (random-phred))) result)) + +(defun random-rna-string (n) + (let ((result (make-string n))) + (dotimes (i n) + (setf (char result i) (random-rna-base))) + result)) + +(defcommand random-rna (n) ((:integer "Length: ")) + (pbcopy (random-rna-string n))) + + (defun random-dna-string (n) (let ((result (make-string n))) (dotimes (i n) - (setf (char result i) (random-base))) + (setf (char result i) (random-dna-base))) result)) (defcommand random-dna (n) ((:integer "Length: ")) (pbcopy (random-dna-string n))) + (defun random-fasta-string (entries entry-length) (str:join #\newline (loop :for i :from 0 :below entries :collect (format nil ">seq ~D" i) :collect (random-dna-string entry-length)))) +(defcommand random-fasta + (entries entry-length) + ((:integer "Entries: ") + (:integer "Entry Length: ")) + (check-type entries (integer 1 *)) + (check-type entry-length (integer 1 *)) + (pbcopy (random-fasta-string entries entry-length))) + + (defun random-fastq-string (entries entry-length) (str:join #\newline (loop :for i :from 0 :below entries @@ -36,14 +60,6 @@ :collect "+" :collect (random-phred-string entry-length)))) -(defcommand random-fasta - (entries entry-length) - ((:integer "Entries: ") - (:integer "Entry Length: ")) - (check-type entries (integer 1 *)) - (check-type entry-length (integer 1 *)) - (pbcopy (random-fasta-string entries entry-length))) - (defcommand random-fastq (entries entry-length) ((:integer "Entries: ") diff -r c0d31d738157 -r 581345d6b360 stumpwm/key-mapping.lisp --- a/stumpwm/key-mapping.lisp Mon Mar 02 13:12:13 2026 -0500 +++ b/stumpwm/key-mapping.lisp Mon Jun 29 12:50:56 2026 -0400 @@ -41,12 +41,11 @@ ("H-O" "spotify") ("H-o" "files") ("H-t" "zoom-meeting") - ("H-P" "papers") ("F26" "prev") ("S-F26" "next") ("H-q" "exec lock-screen") ("H-y" "screenshot") - ("H-Y" "delayed-screenshot") + ("H-Y" "exec switch-yubikey") ("H-r" "rain") ("H-e" "budget") ("H-E" "spend") diff -r c0d31d738157 -r 581345d6b360 vim/custom-dictionary.utf-8.add --- a/vim/custom-dictionary.utf-8.add Mon Mar 02 13:12:13 2026 -0500 +++ b/vim/custom-dictionary.utf-8.add Mon Jun 29 12:50:56 2026 -0400 @@ -574,3 +574,11 @@ FAST5 POD5 nondeterministic +Sniffles2 +hg38 +hg19 +GIAB +Truvari +bcftools +hg37 +LLQR diff -r c0d31d738157 -r 581345d6b360 vim/vimrc --- a/vim/vimrc Mon Mar 02 13:12:13 2026 -0500 +++ b/vim/vimrc Mon Jun 29 12:50:56 2026 -0400 @@ -779,6 +779,32 @@ augroup END " }}} +" FASTQ {{{ + +function! SelectFASTQRead() " {{{ + execute "normal! $?^@\V3j" +endfunction " }}} + +function! MinimeraRead() " {{{ + execute "silent '<,'>! \lG\hG" +endfunction " }}} + +augroup ft_fastq + au! + + autocmd BufNewFile,BufRead *.fastq set filetype=fastq + + au FileType fastq setlocal nowrap + + au FileType fastq xnoremap ir :call SelectFASTQRead() + au FileType fastq xnoremap ar :call SelectFASTQRead() + au FileType fastq onoremap ir :call SelectFASTQRead() + au FileType fastq onoremap ar :call SelectFASTQRead() + + au FileType fastq nmap m var:silent '<,'>w !minimera-stdin.sh +augroup END + +" }}} " Firefox {{{ augroup ft_firefox