d7ff43fdbd408928d1d0b66a1f791e4635032c47
markd
  Sun Feb 20 08:44:04 2022 -0800
add program to take repeat masker .align.tsv files and convert to PSL for use with pslMap

diff --git src/hg/utils/rmskAlignToPsl/tests/makefile src/hg/utils/rmskAlignToPsl/tests/makefile
new file mode 100644
index 0000000..84c980e
--- /dev/null
+++ src/hg/utils/rmskAlignToPsl/tests/makefile
@@ -0,0 +1,30 @@
+kentSrc = ../../../..
+include ../../../../inc/common.mk
+
+rmskAlignToPsl = ${DESTBINDIR}/rmskAlignToPsl
+
+# input/hg38.fa.align.tsv is from Dfam_2.0
+
+
+all::
+
+test:: hg38Test mm39Test  mm39ProbTest
+
+hg38Test: mkout
+	${rmskAlignToPsl} input/hg38.align.tsv output/$@.psl
+	diff expected/$@.psl output/$@.psl
+
+mm39Test: mkout
+	${rmskAlignToPsl} input/mm39.align.tsv output/$@.psl
+	diff expected/$@.psl output/$@.psl
+
+mm39ProbTest: mkout
+	${rmskAlignToPsl} input/mm39.prob.align.tsv output/$@.psl >output/$@.err 2>&1
+	diff expected/$@.psl output/$@.psl
+	diff expected/$@.err output/$@.err
+
+mkout:
+	@mkdir -p output
+
+clean::
+	rm -rf output