From f765c6f41edfb158be77e69758ddf19fb24529ce Mon Sep 17 00:00:00 2001 From: Celine Mercier Date: Sat, 6 Jul 2019 16:29:32 +0200 Subject: [PATCH] obi alignpairedend: fixed a bug where first seq was kept in result view instead of consensus seq --- python/obitools3/libalign/_solexapairend.pyx | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/python/obitools3/libalign/_solexapairend.pyx b/python/obitools3/libalign/_solexapairend.pyx index 634a0cc..11f96aa 100755 --- a/python/obitools3/libalign/_solexapairend.pyx +++ b/python/obitools3/libalign/_solexapairend.pyx @@ -5,7 +5,7 @@ from cpython cimport array from .solexapairend import iterOnAligment from .shifted_ali cimport Ali_shifted -from obitools3.dms.capi.obiview cimport Obiview_p, QUALITY_COLUMN, \ +from obitools3.dms.capi.obiview cimport Obiview_p, QUALITY_COLUMN, NUC_SEQUENCE_COLUMN, \ obi_set_qual_int_with_elt_idx_and_col_p_in_view, \ obi_set_str_with_elt_idx_and_col_p_in_view @@ -233,7 +233,8 @@ def buildConsensus(ali, seq, ref_tags=None): seq[b'mode']=b'alignment' for tag in ref_tags: - if tag != REVERSE_SEQ_COLUMN_NAME and tag != REVERSE_QUALITY_COLUMN_NAME: + if tag != REVERSE_SEQ_COLUMN_NAME and tag != REVERSE_QUALITY_COLUMN_NAME and \ + tag != NUC_SEQUENCE_COLUMN and tag != QUALITY_COLUMN: seq[tag] = ref_tags[tag] return seq