alignpairedend and ngsfilter: ids of original sequences are now kept

python/obitools3/commands/alignpairedend.pyx

@@ -234,6 +234,10 @@ def run(config):
 
         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:
             seqF = entries[i]
         else:

python/obitools3/commands/ngsfilter.pyx

@@ -265,6 +265,10 @@ cdef tuple annotate(sequences, infos, no_tags, verbose=False):
     not_aligned = len(sequences) > 1
     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:
         sequences[1] = sequences[1].clone()
         sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq             # used by alignpairedend tool

src/.gitignore

@@ -3,3 +3,4 @@
 /cmake_install.cmake
 /libcobitools3.dylib
 /Makefile
+/build/