824df26b6320b692d629566c5a10b15004da82ce
lrnassar
  Tue Sep 29 16:09:00 2026 -0700
addProteinSequence in mavemdLib translates each transcript's CDS from
hg38.2bit so makeMaveMdVariants can check every projected codon against the
reference residue its own HGVS term asserts; the existing comparison against
MaveDB's genomic mapping only reaches the 3% of projected items that carry
both terms, because 18 of the 40 protein accessions have no genomic-route
variants at all. 39 of 40 accessions match at 0.000%; NP_689629.2 (FKRP) has
99 nonsense terms numbered one codon downstream of their own reference
residue, which still reach mavemdVar through MaveDB's genomic mapping but are
dropped from mavemdMap, which places columns from the protein term and has no
fallback. The haplotype test now also reads hgvs_nt, since PTEN
00000054-a-1 states 1,236 haplotypes as c.[1207G>T;1209C>T] with no protein
term and they were counted as rejected submissions, making both figures in
the makeDoc wrong. assayLine runs the heatmap legend through asciiText
because bedField turns the en dash in three MaveDB titles into – and
the legend is drawn as raster text; clinGenId links to by_canonicalid rather
than /allele, which serves JSON to a browser, matching human/civic.ra; the
generated filter fragment no longer emits the blank line after each group
that the makeDoc itself warns ends a stanza; and runBuild.sh tails the log on
failure instead of dying silently under set -e. Also reworded the grey legend
entry, which said no threshold was reached in either direction but covers
6,656 normal and 145 abnormal items, alphabetized the references, and fixed
stale counts in the makeDoc. Caught by Claude review of 29af14b, fcf788d and
97c7de5. refs #38407 refs #37800

diff --git src/hg/makeDb/scripts/mavemd/runBuild.sh src/hg/makeDb/scripts/mavemd/runBuild.sh
index c5d0dda0624..50ad3b2d7e4 100755
--- src/hg/makeDb/scripts/mavemd/runBuild.sh
+++ src/hg/makeDb/scripts/mavemd/runBuild.sh
@@ -1,43 +1,47 @@
 #!/bin/bash
 # Build both MaveMD tracks for hg38 from a fetchMaveMd.py download.
 #
 #   runBuild.sh <downloadDir> <buildDir>
 #
 # Produces, in <buildDir>: mavemdVar.bb (one item per variant per score set) and
 # mavemdMap.bb (one variant effect map per score set), plus mavemdFilters.ra, the
 # generated trackDb filterValues block, and a log per stage.
 set -e
 set -o pipefail
 export PATH=$PATH:$HOME/bin/x86_64
 
 DOWNLOAD=${1:?usage: runBuild.sh <downloadDir> <buildDir>}
 BUILD=${2:?usage: runBuild.sh <downloadDir> <buildDir>}
 SCRIPTS=$(cd "$(dirname "$0")" && pwd)
 CHROMSIZES=/hive/data/genomes/hg38/chrom.sizes
 
 mkdir -p "$BUILD"
 cd "$BUILD"
 
 echo "[$(date +%T)] 1. per-variant bed"
+# set -e would otherwise kill the script before the tail, so a build that aborts on one
+# of the coordinate checks prints nothing at all about why.
 "$SCRIPTS/makeMaveMdVariants.py" "$DOWNLOAD" mavemdVar.bed \
-    --raFragment mavemdFilters.ra --workDir . 2> buildVar.log
+    --raFragment mavemdFilters.ra --workDir . 2> buildVar.log \
+    || { echo "makeMaveMdVariants.py failed:"; tail -n 25 buildVar.log; exit 1; }
 tail -n 14 buildVar.log
 
 echo "[$(date +%T)] 2. heatmap bed"
-"$SCRIPTS/makeMaveMdHeatmap.py" "$DOWNLOAD" mavemdMap.bed 2> buildMap.log
+"$SCRIPTS/makeMaveMdHeatmap.py" "$DOWNLOAD" mavemdMap.bed 2> buildMap.log \
+    || { echo "makeMaveMdHeatmap.py failed:"; tail -n 25 buildMap.log; exit 1; }
 tail -n 9 buildMap.log
 
 echo "[$(date +%T)] 3. sort"
 bedSort mavemdVar.bed mavemdVar.sorted.bed
 bedSort mavemdMap.bed mavemdMap.sorted.bed
 
 echo "[$(date +%T)] 4. bigBed"
 bedToBigBed -type=bed12+34 -tab -as="$SCRIPTS/mavemdVariants.as" \
     -extraIndex=name,clinGenId,variantUrn \
     mavemdVar.sorted.bed "$CHROMSIZES" mavemdVar.bb 2>&1 | tail -2
 bedToBigBed -type=bed12+20 -tab -as="$SCRIPTS/mavemdHeatmap.as" \
     mavemdMap.sorted.bed "$CHROMSIZES" mavemdMap.bb 2>&1 | tail -2
 
 echo "[$(date +%T)] done"
 bigBedInfo mavemdVar.bb | egrep 'itemCount|basesCovered|fieldCount'
 bigBedInfo mavemdMap.bb | egrep 'itemCount|basesCovered|fieldCount'