e813f6c7cfd2f8f110266c0824062964322d62a3
markd
  Wed Sep 20 00:01:21 2023 -0700
fixed problems handling overlapping PSL blocks caused by protein to NA alignemtns. Now handles internal coversions create overlapoing blocks

diff --git src/utils/pslMap/tests/input/README src/utils/pslMap/tests/input/README
index 53c45f9..d3bde0e 100644
--- src/utils/pslMap/tests/input/README
+++ src/utils/pslMap/tests/input/README
@@ -1,35 +1,40 @@
 
 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
+
+
+annotProt.psl -> protGencode.psl
+  swissprot annotation to protein and proten to transcript
+  this created an invalid PSL when converting AA to NA