29f88e9827e33081a9e4c4db1c6dcca6542f7ccd
kent
  Sun Jun 19 22:29:39 2022 -0700
First cut of next generation liftOver chain maker.  This one is meant to handle swapping in alternate haplotypes properly, even when, as is the case with the HLA locus in the t2t, more than one alt is moved.  Still needs lots of testing and polishing, but finishes and makes something semi-plausable on t2t's chr6 going against hg38's chr6 + alts.

diff --git src/hg/oneShot/testLiftRechainer/makefile src/hg/oneShot/testLiftRechainer/makefile
new file mode 100644
index 0000000..97bd9e9
--- /dev/null
+++ src/hg/oneShot/testLiftRechainer/makefile
@@ -0,0 +1,3 @@
+kentSrc = ../../..
+A = testLiftRechainer
+include $(kentSrc)/inc/userApp.mk