1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/c54ebfe2c008/
changeset: c54ebfe2c008
user: jgoecks
date: 2012-12-21 22:08:16
summary: Fixes for sorting and merging genomic regions during visual analysis.
affected #: 1 file
diff -r 692a1e8b69998d99465838cb5c8b1d56f3a37d2d -r
c54ebfe2c0086b6e690e98a958e2d41ecf722bec lib/galaxy/webapps/galaxy/api/tools.py
--- a/lib/galaxy/webapps/galaxy/api/tools.py
+++ b/lib/galaxy/webapps/galaxy/api/tools.py
@@ -158,17 +158,16 @@
if len( regions ) > 1:
# Sort by chrom name, start so that data is not fetched out of
order.
- regions.sort( key=lambda r: r.chrom )
- regions.sort( key=lambda r: r.start )
-
+ regions = sorted(regions, key=lambda r: (r.chrom.lower(), r.start))
+
# Merge overlapping regions so that regions do not overlap
# and hence data is not included multiple times.
prev = regions[0]
cur = regions[1]
index = 1
while True:
- if cur.start <= prev.end:
- # Found overlapping regions, so join them.
+ if cur.chrom == prev.chrom and cur.start <= prev.end:
+ # Found overlapping regions, so join them into prev.
prev.end = cur.end
del regions[ index ]
else:
@@ -182,7 +181,7 @@
break
else:
cur = regions[ index ]
-
+
run_on_regions = True
# Dataset check.
Repository URL:
https://bitbucket.org/galaxy/galaxy-central/
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