418b11748d3ae9c1217714a92d4a7fe46b6819b9
chmalee
  Thu May 28 17:14:54 2020 -0700
Added a few more trios to the 1000 Genomes trio track QA ready, refs #25582

diff --git src/hg/makeDb/tgpTrio/loadTables.sh src/hg/makeDb/tgpTrio/loadTables.sh
new file mode 100755
index 0000000..869205c
--- /dev/null
+++ src/hg/makeDb/tgpTrio/loadTables.sh
@@ -0,0 +1,24 @@
+#!/bin/bash
+
+# for each trio in the ./output dir, install files into /gbdb and load up a table with the pointers
+p="/gbdb/hg38/1000Genomes/trio/"
+for d in output/*
+do
+    # the '##' below is a bashism for deleting the first leading match
+    # (it deletes 'output/' from whatever is in $d)
+    tbl=${d##output/}
+    mkdir -p ${p}${tbl}
+    cd ${d}
+    ln -s `pwd`/*.vcf.gz* /gbdb/hg38/1000Genomes/trio/${tbl}
+    cp /dev/null tgp${tbl}.txt
+    for c in {1..22}
+    do
+        f=${tbl}Trio.chr${c}.vcf.gz
+        echo -e "${p}${tbl}/${f}\tchr${c}" >> tgp${tbl}.txt
+    done
+    # don't forget chrX
+    f=${tbl}Trio.chrX.vcf.gz
+    echo -e "${p}${tbl}/${f}\tchrX" >> tgp${tbl}.txt
+    hgLoadSqlTab hg38 tgp${tbl} ~/kent/src/hg/lib/bbiChroms.sql tgp${tbl}.txt
+    cd ../..
+done