c8174ac2c2237b3f8f24766ca50348487ba94fa7
galt
  Wed Aug 15 14:48:47 2012 -0700
bedPileUps is a new utility for finding where how many pileups there are in input including the locations and the sizes, with a summary maximum and its location, plus average pileup size.  Matching is on chrom/start/end with name as an additional option for uniqueness.
diff --git src/utils/bedPileUps/checkBedTablePileUps.csh src/utils/bedPileUps/checkBedTablePileUps.csh
new file mode 100755
index 0000000..8141e14
--- /dev/null
+++ src/utils/bedPileUps/checkBedTablePileUps.csh
@@ -0,0 +1,13 @@
+#!/bin/tcsh
+# find tables with pileups
+if ("$1" == "") then
+    echo "must specify the database"
+    exit 1
+endif
+if ("$2" == "") then
+    echo "must specify the table"
+    exit 1
+endif
+# assumes that there is a bin column that needs cutting out
+#DEBUG IGNORE NAMES hgsql $1 -BN -e "select * from $2" | cut -f 2- | bedPileUps stdin > $1.$2.txt
+hgsql $1 -BN -e "select * from $2" | cut -f 2- | bedPileUps -name stdin > $1.$2.txt
