ngsfilter and ecopcr: now check for primers too long for apat library to

handle (31bp max) and switch to version 3.0.1b23

python/obitools3/commands/ngsfilter.pyx

@@ -24,6 +24,9 @@ from cpython.exc cimport PyErr_CheckSignals
 from io import BufferedWriter
 
 
+MAX_PAT_LEN = 31
+
+
 __title__="Assign sequence records to the corresponding experiment/sample based on DNA tags and primers"
 
 
@@ -84,6 +87,8 @@ class Primer:
         @type direct:
         '''
         
+        assert len(sequence) <= MAX_PAT_LEN, "Primer %s is too long, 31 bp max" % sequence
+        
         assert sequence not in Primer.collection        \
             or Primer.collection[sequence]==taglength,  \
             "Primer %s must always be used with tags of the same length" % sequence
@@ -271,7 +276,7 @@ cdef tuple annotate(sequences, infos, no_tags, verbose=False):
 
     if not_aligned:
         sequences[1] = sequences[1].clone()
-        sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq             # used by alignpairedend tool
+        sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq        # used by alignpairedend tool
         sequences[0][REVERSE_QUALITY_COLUMN] = sequences[1].quality     # used by alignpairedend tool
 
     for seq in sequences:
@@ -299,7 +304,7 @@ cdef tuple annotate(sequences, infos, no_tags, verbose=False):
             directmatch.append((p, p(seq, same_sequence=not new_seq, pattern=pattern), seq, p))
             new_seq = False
             pattern+=1
-    
+        
     # Choose match closer to the start of (one of the) sequence(s)
     directmatch = sorted(directmatch, key=sortMatch)
     all_direct_matches = directmatch

python/obitools3/version.py

@@ -1,5 +1,5 @@
 major = 3
 minor = 0
-serial= '1b22'
+serial= '1b23'
 
 version ="%d.%d.%s" % (major,minor,serial)