From 1d38f5a11dd306fa33f1ec38ec310a1a092145b9 Mon Sep 17 00:00:00 2001 From: DimitriMeistermann Date: Thu, 8 Jul 2021 13:01:44 +0300 Subject: [PATCH] Update leafcutter_cluster_regtools.py On new version of human genomes (Grch38), it is possible to get contigs (the generalisation of the concept of chromosome) with no junctions, and hence the program stops. This correction pass the contig if it is the case. --- clustering/leafcutter_cluster_regtools.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/clustering/leafcutter_cluster_regtools.py b/clustering/leafcutter_cluster_regtools.py index adf7fb3..e34fb5e 100755 --- a/clustering/leafcutter_cluster_regtools.py +++ b/clustering/leafcutter_cluster_regtools.py @@ -69,6 +69,8 @@ def pool_junc_reads(flist, options): read_ks.sort() sys.stderr.write("%s:%s.."%chrom) + if len(read_ks)<1 : continue #empty contig + clu = cluster_intervals(read_ks)[0] for cl in clu: