Merge branch 'documentation/JAL-3766_relnotes' into releases/Release_2_11_1_Branch

[jalview.git] / examples / testdata / exonerateoutput.gff

diff --git a/examples/testdata/exonerateoutput.gff b/examples/testdata/exonerateoutput.gff
index 3ea68dc..d3b5f9b 100644 (file)
--- a/examples/testdata/exonerateoutput.gff
+++ b/examples/testdata/exonerateoutput.gff
@@ -1,3 +1,7 @@
+# (exonerate delimits GFF with [START|END] OF GFF DUMP)
+# --- START OF GFF DUMP ---
+#
+#
 ##gff-version 2
 ##source-version exonerate:protein2genome:local 2.2.0
 ##date 2015-01-16
@@ -9,5 +13,8 @@
 contig_1146    exonerate:protein2genome:local  gene    8534    11269   3652    -       .       gene_id 0 ; sequence DDB_G0269124 ; gene_orientation .
 contig_1146    exonerate:protein2genome:local  cds     8534    11269   .       -       .       
 contig_1146    exonerate:protein2genome:local  exon    8534    11269   .       -       .       insertions 3 ; deletions 6
+#TODO need to understand why GFF features is from 11269 but Align is from 11270
 contig_1146    exonerate:protein2genome:local  similarity      8534    11269   3652    -       .       alignment_id 0 ; Query DDB_G0269124 ; Align 11270 143 120 ; Align 11150 187 282 ; Align 10865 281 888 ; Align 9977 578 1068 ; Align 8909 935 375
+# and a made-up alignment to a sequence in exonerateseqs.fa
+contig_1146    exonerate:protein2genome:local  similarity      8534    11269   3652    -       .       alignment_id 0 ; Query DDB_G0280897 ; Align 11270 143 120 
 # --- END OF GFF DUMP ---