--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seqrequester/src/utility/scripts/build_initial_repo.sh	Sat Jul 13 12:39:06 2024 +0000
@@ -0,0 +1,75 @@
+#!/bin/sh
+
+#  You do not want to run this.  It was used to create the initial repo by
+#  extracting the relevant bits from Canu and renaming things.
+
+if [ `pwd` != "/scratch/git/canu-test" ] ; then
+  echo Wrong directory.
+  exit
+fi
+
+echo DELETE
+rm -rf .git *
+
+echo SYNC
+rsync -a ../canu-orig/ .
+
+echo REWRITE
+../git-filter-repo/git-filter-repo --replace-refs delete-no-add \
+  --path kmer/libutil \
+  --path kmer/libkmer \
+  --path kmer/libbio \
+  --path src/AS_UTL \
+  --path src/AS_global.C \
+  --path src/AS_global.H \
+  --path src/AS_global.c \
+  --path src/AS_global.h \
+  --path src/utility \
+  --path src/canu_version_update.pl \
+  --path src/Makefile \
+  --path src/main.mk \
+  --path 'README.license.GPL' \
+  --path 'README.licenses' \
+  --path 'README.md'
+
+../git-filter-repo/git-filter-repo \
+  --path src/AS_UTL/Makefile \
+  --path src/AS_UTL/main.mk --invert-paths
+
+../git-filter-repo/git-filter-repo \
+  --path-rename src/canu_version_update.pl:scripts/version_update.pl
+
+../git-filter-repo/git-filter-repo \
+  --path-rename src/AS_UTL:src/utility
+
+../git-filter-repo/git-filter-repo --path-rename                     src/AS_global.H:src/utility/runtime.H
+../git-filter-repo/git-filter-repo --path-rename                     src/AS_global.C:src/utility/runtime.C
+../git-filter-repo/git-filter-repo --path-rename                     src/AS_global.h:src/utility/runtime.h
+../git-filter-repo/git-filter-repo --path-rename                     src/AS_global.c:src/utility/runtime.c
+
+../git-filter-repo/git-filter-repo --path-rename              src/utility/bitsTest.C:src/tests/bitsTest.C
+../git-filter-repo/git-filter-repo --path-rename             src/utility/bitsTest.mk:src/tests/bitsTest.mk
+../git-filter-repo/git-filter-repo --path-rename             src/utility/filesTest.C:src/tests/filesTest.C
+../git-filter-repo/git-filter-repo --path-rename            src/utility/filesTest.mk:src/tests/filesTest.mk
+../git-filter-repo/git-filter-repo --path-rename      src/utility/intervalListTest.C:src/tests/intervalListTest.C
+../git-filter-repo/git-filter-repo --path-rename     src/utility/intervalListTest.mk:src/tests/intervalListTest.mk
+../git-filter-repo/git-filter-repo --path-rename           src/utility/loggingTest.C:src/tests/loggingTest.C
+../git-filter-repo/git-filter-repo --path-rename          src/utility/loggingTest.mk:src/tests/loggingTest.mk
+../git-filter-repo/git-filter-repo --path-rename  src/utility/memoryMappedFileTest.C:src/tests/memoryMappedFileTest.C
+../git-filter-repo/git-filter-repo --path-rename         src/utility/mt19937arTest.C:src/tests/mt19937arTest.C
+../git-filter-repo/git-filter-repo --path-rename            src/utility/stddevTest.C:src/tests/stddevTest.C
+../git-filter-repo/git-filter-repo --path-rename           src/utility/stddevTest.mk:src/tests/stddevTest.mk
+../git-filter-repo/git-filter-repo --path-rename           src/utility/stringsTest.C:src/tests/stringsTest.C
+../git-filter-repo/git-filter-repo --path-rename              src/utility/testRand.C:src/tests/randTest.C
+
+
+#  Delete all replace refs, since I can't seem to get them disabled.
+git replace -d `git replace -l` > refs-deleted 2>&1
+
+
+cp -fp ../NEW-Makefile          src/Makefile
+cp -fp ../NEW-main.mk           src/main.mk
+cp -fp ../NEW-runtime.C         src/utility/runtime.C
+cp -fp ../NEW-runtime.H         src/utility/runtime.H
+cp -fp ../NEW-types.H           src/utility/types.H
+cp -fp ../NEW-version_update.pl scripts/version_update.pl