726a4c9c82592c662ae6b8c715e67b783c95beb3
angie
  Mon Nov 18 13:45:42 2019 -0800
Instead of dropping rs IDs that have incomplete frequency data, add two new ucscNotes: freqIncomplete and freqNotMapped.  refs #23283

diff --git src/hg/lib/bigDbSnp.c src/hg/lib/bigDbSnp.c
index 9fd0390..62b7548 100644
--- src/hg/lib/bigDbSnp.c
+++ src/hg/lib/bigDbSnp.c
@@ -319,33 +319,38 @@
       "Variant is in ClinVar with reports of both benign and pathogenic significance." },
     { bdsClinvarPathogenic,
       "Variant is in ClinVar with clinical significance of pathogenic and/or likely pathogenic." },
     { bdsClusterError,
       "This variant has the same start, end and class as another variant; "
       "they probably should have been merged into one variant." },
     { bdsCommonAll,
       "Variant is \"common\", i.e. has a Minor Allele Frequency of at least 1% "
       "in all projects reporting frequencies." },
     { bdsCommonSome,
       "Variant is \"common\", i.e. has a Minor Allele Frequency of at least 1% "
       "in some, but not all, projects reporting frequencies." },
     { bdsDiffMajor,
       "Different frequency sources have different major alleles "
       "(see table of allele frequencies above)." },
+    { bdsFreqIncomplete,
+      "At least one project's frequency data is incomplete (only one allele reported)." },
     { bdsFreqIsAmbiguous,
       "At least one allele reported by at least one project "
       "contains an IUPAC ambiguous base (e.g. 'R' for 'A or G')." },
+    { bdsFreqNotMapped,
+      "At least one project reported frequencies on a different assembly, for which dbSNP does not "
+      "provide a mapping.  The mapping on this assembly may have an issue." },
     { bdsFreqNotRefAlt,
       "The reference genome allele is not the major allele in at least one project." },
     { bdsMultiMap,
       "This variant has been mapped to more than one distinct genomic location." },
     { bdsOtherMapErr,
       "Another mapping of this variant has illegal coordinates implying indel mapping error." },
     { bdsOverlapDiffClass,
       "This variant overlaps another variant with a different type/class." },
     { bdsOverlapSameClass,
       "This variant overlaps another with the same type/class but different start/end." },
     { bdsRareAll,
       "Variant is \"rare\", i.e. has a Minor Allele Frequency of less than 1% "
       "in all projects reporting frequencies, or has no frequency data." },
     { bdsRareSome,
       "Variant is \"rare\", i.e. has a Minor Allele Frequency of less than 1% "