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alignpairedend and ngsfilter: ids of original sequences are now kept

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This commit is contained in:
Celine Mercier
2022-09-21 11:32:19 +12:00
parent 55ada80500
commit 02e9df3ad1
3 changed files with 9 additions and 0 deletions
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4
python/obitools3/commands/alignpairedend.pyx
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@ -233,6 +233,10 @@ def run(config):
PyErr_CheckSignals() PyErr_CheckSignals()
consensus = o_view[i] consensus = o_view[i]
if two_views:
consensus[b"R1_parent"] = forward[i].id
consensus[b"R2_parent"] = reverse[i].id
if not two_views: if not two_views:
seqF = entries[i] seqF = entries[i]

4
python/obitools3/commands/ngsfilter.pyx
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@ -264,6 +264,10 @@ cdef tuple annotate(sequences, infos, no_tags, verbose=False):
not_aligned = len(sequences) > 1 not_aligned = len(sequences) > 1
sequences[0] = sequences[0].clone() sequences[0] = sequences[0].clone()
if not_aligned:
sequences[0][b"R1_parent"] = sequences[0].id
sequences[0][b"R2_parent"] = sequences[1].id
if not_aligned: if not_aligned:
sequences[1] = sequences[1].clone() sequences[1] = sequences[1].clone()

1
src/.gitignore vendored
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@ -3,3 +3,4 @@
/cmake_install.cmake /cmake_install.cmake
/libcobitools3.dylib /libcobitools3.dylib
/Makefile /Makefile
/build/