The following files are in here because they were .c files that were not in the makefile.

encodeErge5race.c
encodeErgeBinding.c
encodeErgeDNAseI.c
encodeErgeExpProm.c
encodeErgeInVitroFoot.c
encodeErgeMethProm.c
encodeErgeStableTransf.c
encodeErgeSummary.c
encodeErgeTransTransf.c
encodePrimateAlleles.c

The following files are in here because they are .sql files with no .as or .c.  What could they be used for?

encodeBuPromCerebrum.sql
encodeBuPromColon.sql
encodeBuPromHeart.sql
encodeBuPromKidney.sql
encodeBuPromLiver.sql
encodeBuPromLung.sql
encodeBuPromSkMuscle.sql
encodeBuPromSpleen.sql
encodeBuPromStomach.sql
encodeBuPromTestis.sql

The following files are in here because we are no longer accepting or displaying the type.

shortFrags.as
shortFrags.sql
