From 2975672b77909cd454a25361b1aba4090da93007 Mon Sep 17 00:00:00 2001 From: Ivan Blagoev Topolsky Date: Wed, 5 Jun 2024 15:48:18 +0200 Subject: [PATCH] [wip] process soft-clipped reads --- scripts/paired_end_read_merger | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/scripts/paired_end_read_merger b/scripts/paired_end_read_merger index d8bea6d..6503358 100755 --- a/scripts/paired_end_read_merger +++ b/scripts/paired_end_read_merger @@ -327,7 +327,8 @@ def fuse_reads(argv): if prev is not None: if prev.qname == read.qname: #if (read.pos > 0 and ( ('D' in read.cigarstring or 'D' in prev.cigarstring) and not 'S' in read.cigarstring and not 'S' in prev.cigarstring) ): - if (read.pos > 0 and ( not 'S' in read.cigarstring and not 'S' in prev.cigarstring) ): # for properly aligned, skipping unaligned, skipping softclipping + #if (read.pos > 0 and ( not 'S' in read.cigarstring and not 'S' in prev.cigarstring) ): # for properly aligned, skipping unaligned, skipping softclipping + if read.pos > 0 : # for properly aligned, skipping unaligned fused = read_fusion(prev, read, reference, samfile.header) i = i + 1 cl = query_len(fused.cigarstring)