02336754147822f5aa61ba13277123b2cc629001
markd
  Thu May 20 08:38:55 2021 -0700
Moved pslMap, pslMapPostChain, pslRc, pslSwap to src/utils, as they do not have hg/lib dependencies.

diff --git src/utils/pslMap/tests/input/README src/utils/pslMap/tests/input/README
new file mode 100644
index 0000000..53c45f9
--- /dev/null
+++ src/utils/pslMap/tests/input/README
@@ -0,0 +1,35 @@
+
+protein->mRNA->genome tests:
+    *MRnaProt.map - map of mRNA to associated protein
+    *Prot.fa  - protein sequence
+    *MRna.fa  - mRNA sequence
+    *MRna.psl - mRNA alignment to genome
+    *ProtMRna.blast - blast alignment of protein to mRNA (plus some other hits)
+
+
+  - alignments of protein to mrna were done with:
+    formatdb -i kgMRna.fa -p F
+    blastall -S 2 -p tblastn -d kgMRna.fa -i kgProt.fa -o kgProtMRna.blast
+
+  - test PSLs are generated from tblastn output in this directory when
+    test is run to allow for changes in blastToPsl
+
+  - test sets:
+    - kg*: input: basic set of mRNAs and proteins
+    - gapBoth*: both query and target have a gap between two blocks
+
+mRNA->mRNA->DNA mapping test:
+  pos strand:
+    BC032429, AY211386, AK000004, BX647829, AX810690 -> NM_033086  -> genome
+  neg strand:
+    AB000114, BC046356 -> NM_005014 -> genome
+
+  refSeqGen.psl - refseq to genome alignments
+  mrnaRefSeq.psl - rna to refseq alignments, created with
+        blat -noHead rs.fa gb.fa mrnaRefSeq.psl
+
+  mrnaRefSeqX.psl - rrna to refseq translated alignments, created with
+        blat -noHead -q=rnax -t=dnax rs.fa gb.fa mrnaRefSeqX.psl
+
+retro/parent alignment with -simplifyMappingIds
+  parent.psl, retro.psl from hg18