src/hg/encode/DAFs/GisDnaPet.daf 1.3

Index: src/hg/encode/DAFs/GisDnaPet.daf
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/encode/DAFs/GisDnaPet.daf,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 1000000 -r1.2 -r1.3
--- src/hg/encode/DAFs/GisDnaPet.daf	5 Feb 2009 18:17:23 -0000	1.2
+++ src/hg/encode/DAFs/GisDnaPet.daf	10 Feb 2009 17:18:38 -0000	1.3
@@ -1,36 +1,73 @@
 # Data Agreement File for Genomic DNA PET Ditag project $Revision$
 
 # This file specifies the data agreement between your lab and 
 # the DCC.  It should not be changed unilaterally.
 
 # Lab and general info
 grant             Gingeras
 lab               Gis
 dataType          DnaPet
 variables         cell, fragSize
 assembly          hg18
 dafVersion        0.2.2
 
 # Track/view definition
 view             Tags
 longLabelPrefix  GIS DNA PET Tags
 type             gappedPeak
 hasReplicates    no
 required         no
 
 view             RawSignal
 longLabelPrefix  GIS DNA PET Raw Signal
 type             wig
 hasReplicates    no
 required         no
 
 view             Alignments
 longLabelPrefix  GIS DNA PET Alignments
 type             pairedTagAlign
 hasReplicates    no
 required         yes
 
+# Discordant alignments have pairs on opposite strands of the same chrom, or on different chroms.
+# File formats:- 
+#  - a bed 6 file for the chrom/start/end/name/score/strand for the left & right tags
+#  - a pairedInteraction file for the relationship between left & right tags
+# Note:-
+# We cant capture the sequence of the tag in this format because we need unique names in the name column
+# to specify the relationship between the left & right tags in the pairedInteraction file.
+
+view             DiscordAlign
+longLabelPrefix  GIS DNA PET Discordant Tag Alignments
+type             bed
+hasReplicates    no
+required         no
+
+view             DiscordRel
+longLabelPrefix  GIS DNA PET Discordant Tag Relations
+type             pairedInteraction
+hasReplicates    no
+required         no
+
+# Send the raw seq reads data in either Solexa (fastq) or SOLiD (csfasta+csqual) formats:-
+# Ideally we would be able to check that the data contains either fastq or csfasta+csqual formats
+#   but the DAF control 'required=yes/no' is to simple to specify that.
+
+# Solexa:-
 view             RawData
 type             fastq
 hasReplicates    no
-required         yes
+required         no
+
+# SOLiD:-
+view             RawData2
+type             csfasta
+required         no
+hasReplicates    no
+
+view             RawData3
+type             csqual
+required         no
+hasReplicates    no
+