9cc55e7992e4a98ef3a3336e12e78a583a7a56a1
chmalee
  Mon Jul 12 17:07:48 2021 -0700
Allow lower case first letter of 3-letter amino acid code in psueudo hgvs gene searches, refs #15554

diff --git src/hg/lib/hgHgvs.c src/hg/lib/hgHgvs.c
index 7ef08da..a3af8af 100644
--- src/hg/lib/hgHgvs.c
+++ src/hg/lib/hgHgvs.c
@@ -83,31 +83,32 @@
 //                                        ...           1-based end anchor base offset
 //                                            .......   optional offset separator and offset
 //                                            ...       intron offset separator
 //                                                ...   intron offset number
 
 // It's pretty common for users to omit the '.' so if it's missing but the rest of the regex fits,
 // roll with it.
 #define hgvsCDotPosExp "c\\.?" hgvsCdsPosExp
 #define hgvsGMDotPosExp "([gm])\\.?" hgvsGenoPosExp
 #define hgvsNDotPosExp "n\\.?" hgvsCdsPosExp
 // Not supporting RDot at this point because r. terms may use either n. or c. numbering!
 // #define hgvsRDotPosExp "r\\.?" hgvsCdsPosExp
 
 // Protein substitution regex
 #define aa3Exp "Ala|Arg|Asn|Asp|Cys|Gln|Glu|Gly|His|Ile|Leu|Lys|Met|Phe|Pro|Ser|Thr|Trp|Tyr|Val|Ter"
-#define hgvsAminoAcidExp "[ARNDCQEGHILKMFPSTWYVX*]|" aa3Exp
+#define aa3ExpLower "ala|arg|asn|asp|cys|gln|glu|gly|his|ile|leu|lys|met|phe|pro|ser|thr|trp|tyr|val|ter"
+#define hgvsAminoAcidExp "[ARNDCQEGHILKMFPSTWYVX*]|" aa3Exp "|" aa3ExpLower
 #define hgvsAminoAcidSubstExp "(" hgvsAminoAcidExp ")" posIntExp "(" hgvsAminoAcidExp "|=)"
 #define hgvsPDotSubstExp "p\\.\\(?" hgvsAminoAcidSubstExp "\\)?"
 //                                 ...                                  // original sequence
 //                                              ......                  // 1-based position
 //                                                           ...        // replacement sequence
 
 // Protein range (or just single pos) regex
 #define hgvsAaRangeExp "(" hgvsAminoAcidExp ")" posIntExp "(_(" hgvsAminoAcidExp ")" posIntExp ")?(.*)"
 #define hgvsPDotRangeExp "p\\.\\(?" hgvsAaRangeExp "\\)?"
 //  original start AA           ...
 //  1-based start position                       ...
 //  optional range sep and AA+pos                          .....................................
 //  original end AA                                              ...
 //  1-based end position                                                          ...
 //  change description                                                                    ...