Added the kmer filter to LCS alignments, and now obiblobs containing

encoded sequences are directly put in int16_t arrays for the alignment

python/obitools3/commands/align.pyx

@@ -46,7 +46,7 @@ def addOptions(parser):
                        metavar='<ALIGNMENT TYPE>',
                        default='lcs',
                        type=str,
-                       help="Compute alignment using the LCS method.")
+                       help="Compute alignment using the LCS method (default).")
  
     group.add_argument('--threshold','-t',
                        action="store", dest="align:threshold",
@@ -64,15 +64,15 @@ def addOptions(parser):
 
     group.add_argument('--longest_length','-L',
                        action="store_const", dest="align:reflength",
-                       default="ali",
-                       const="longest",
+                       default=0,
+                       const=1,
                        help="The reference length is the length of the longest sequence."
                             " Default: the reference length is the length of the alignment.")
 
     group.add_argument('--shortest_length','-l',
                        action="store_const", dest="align:reflength",
-                       default="ali",
-                       const="shortest",
+                       default=0,
+                       const=2,
                        help="The reference length is the length of the shortest sequence."
                             " Default: the reference length is the length of the alignment.")
 
@@ -89,9 +89,7 @@ def addOptions(parser):
 
     
 def run(config):
-  
-    #pb = ProgressBar(1, config, seconde=5)  # TODO
-    
+     
     # Open DMS
     d = OBIDMS(config['obi']['defaultdms'])
     
@@ -106,9 +104,9 @@ def run(config):
     # TODO Take other alignment types into account when they'll be implemented
     
     # Call cython alignment function
-    iview.align(oview)
-    
-    repr(oview)
+    iview.align(oview, threshold=config['align']['threshold'], normalize=config['align']['normalize'], reference=config['align']['reflength'], similarity_mode=config['align']['similarity'])
+
+    print(repr(oview))
     
     iview.close()
     oview.close()

python/obitools3/obidms/_obidms.cfiles

@@ -59,5 +59,7 @@
 ../../../src/sse_banded_LCS_alignment.c
 ../../../src/uint8_indexer.h
 ../../../src/uint8_indexer.c
+../../../src/upperband.h
+../../../src/upperband.c
 ../../../src/utils.h
 ../../../src/utils.c

python/obitools3/obidms/_obidmscolumn_bool.cfiles

@@ -59,5 +59,7 @@
 ../../../src/sse_banded_LCS_alignment.c
 ../../../src/uint8_indexer.h
 ../../../src/uint8_indexer.c
+../../../src/upperband.h
+../../../src/upperband.c
 ../../../src/utils.h
 ../../../src/utils.c

python/obitools3/obidms/_obidmscolumn_char.cfiles

@@ -59,5 +59,7 @@
 ../../../src/sse_banded_LCS_alignment.c
 ../../../src/uint8_indexer.h
 ../../../src/uint8_indexer.c
+../../../src/upperband.h
+../../../src/upperband.c
 ../../../src/utils.h
 ../../../src/utils.c

python/obitools3/obidms/_obidmscolumn_float.cfiles

@@ -59,5 +59,7 @@
 ../../../src/sse_banded_LCS_alignment.c
 ../../../src/uint8_indexer.h
 ../../../src/uint8_indexer.c
+../../../src/upperband.h
+../../../src/upperband.c
 ../../../src/utils.h
 ../../../src/utils.c

python/obitools3/obidms/_obidmscolumn_int.cfiles

@@ -59,5 +59,7 @@
 ../../../src/sse_banded_LCS_alignment.c
 ../../../src/uint8_indexer.h
 ../../../src/uint8_indexer.c
+../../../src/upperband.h
+../../../src/upperband.c
 ../../../src/utils.h
 ../../../src/utils.c

python/obitools3/obidms/_obidmscolumn_qual.cfiles

@@ -59,5 +59,7 @@
 ../../../src/sse_banded_LCS_alignment.c
 ../../../src/uint8_indexer.h
 ../../../src/uint8_indexer.c
+../../../src/upperband.h
+../../../src/upperband.c
 ../../../src/utils.h
 ../../../src/utils.c

python/obitools3/obidms/_obidmscolumn_seq.cfiles

@@ -59,5 +59,7 @@
 ../../../src/sse_banded_LCS_alignment.c
 ../../../src/uint8_indexer.h
 ../../../src/uint8_indexer.c
+../../../src/upperband.h
+../../../src/upperband.c
 ../../../src/utils.h
 ../../../src/utils.c

python/obitools3/obidms/_obidmscolumn_str.cfiles

@@ -59,5 +59,7 @@
 ../../../src/sse_banded_LCS_alignment.c
 ../../../src/uint8_indexer.h
 ../../../src/uint8_indexer.c
+../../../src/upperband.h
+../../../src/upperband.c
 ../../../src/utils.h
 ../../../src/utils.c

python/obitools3/obidms/_obiseq.cfiles

@@ -59,5 +59,7 @@
 ../../../src/sse_banded_LCS_alignment.c
 ../../../src/uint8_indexer.h
 ../../../src/uint8_indexer.c
+../../../src/upperband.h
+../../../src/upperband.c
 ../../../src/utils.h
 ../../../src/utils.c

python/obitools3/obidms/_obitaxo.cfiles

@@ -59,5 +59,7 @@
 ../../../src/sse_banded_LCS_alignment.c
 ../../../src/uint8_indexer.h
 ../../../src/uint8_indexer.c
+../../../src/upperband.h
+../../../src/upperband.c
 ../../../src/utils.h
 ../../../src/utils.c