From 00993d4215fef05e591b5ba6b902a589aff46218 Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Mon, 12 Feb 2018 14:42:30 +0100
Subject: [PATCH] Cython API: fixed a bug where the quality format would not be
 read properly from the configuration values

---
 python/obitools3/commands/alignpairedend.pyx |  9 ++++-----
 python/obitools3/uri/decode.pyx              | 10 +++++++---
 2 files changed, 11 insertions(+), 8 deletions(-)

diff --git a/python/obitools3/commands/alignpairedend.pyx b/python/obitools3/commands/alignpairedend.pyx
index 896d7f9..17ab75c 100644
--- a/python/obitools3/commands/alignpairedend.pyx
+++ b/python/obitools3/commands/alignpairedend.pyx
@@ -96,11 +96,11 @@ def run(config):
     logger("info", "obi alignpairedend")
     
     # Open the input
-    finput = open_uri(config["alignpairedend"]["forward"], config)
+    finput = open_uri(config["alignpairedend"]["forward"])
     if finput is None:
         raise Exception("Could not open forward reads")
     forward = finput[1]
-    rinput = open_uri(config["alignpairedend"]["reverse"], config)
+    rinput = open_uri(config["alignpairedend"]["reverse"])
     if rinput is None:
         raise Exception("Could not open reverse reads")
     reverse = rinput[1]
@@ -108,14 +108,13 @@ def run(config):
     if len(forward) != len(reverse):
         raise Exception("Error: the number of forward and reverse reads are different")
     
-    if "index" in config["alignpairedend"]:
-        index = open_uri(config["alignpairedend"]["index"], config)
+    if "index" in config["alignpairedend"]:    # TODO
+        index = open_uri(config["alignpairedend"]["index"])
     else:
         index = None
     
     # Open the output
     output = open_uri(config['obi']['outputURI'],
-                      config,
                       input=False,
                       newviewtype=View_NUC_SEQS)
     if output is None:
diff --git a/python/obitools3/uri/decode.pyx b/python/obitools3/uri/decode.pyx
index 284b995..11b1237 100644
--- a/python/obitools3/uri/decode.pyx
+++ b/python/obitools3/uri/decode.pyx
@@ -62,7 +62,7 @@ def open_dms_element(DMS dms, bytes path,
     if not path:
         return (dms,dms)
     
-    # The URI is target a taxonomy
+    # The URI targets a taxonomy
     # dms:dmspath/taxonomy/taxoname[/taxid]
     if path_parts[0]==b"taxonomy":
         if len(path_parts) > 1:
@@ -74,7 +74,7 @@ def open_dms_element(DMS dms, bytes path,
                 raise MalformedURIException('Malformed Taxonomy URI')
             return (dms,taxo)
 
-    # The URI is target a view
+    # The URI targets a view
     # dms:dmspath/viewname[/columnname|#line|*[/#line|columnname|*[/subcolumn]]]
     
     if create:
@@ -282,7 +282,11 @@ def open_uri(uri,
                 offset=64
         else:
             try:
-                offset=config["obi"]["qualityoffset"]
+                if config["obi"]["qualityformat"][0]=="sanger":
+                    offset=33
+                elif config["obi"]["qualityformat"][0]=="solexa":
+                    offset=64
+                #offset=config["obi"]["qualityoffset"]   # TODO discuss
             except KeyError:
                 offset=33