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 4 -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
@@ -29,8 +29,45 @@
 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
+