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Cython API: fixed a bug in URI decoding and option handling where the

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quality offset would not be read properly
This commit is contained in:
Celine Mercier
2018-05-17 15:10:52 +02:00
parent ffebc6acfb
commit 62614a8538
1 changed files with 6 additions and 5 deletions
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11
python/obitools3/uri/decode.pyx
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@ -66,6 +66,7 @@ def open_dms_element(DMS dms, bytes path,
if not path: if not path:
return (dms,dms) return (dms,dms)
# TODO SHOULD READ AND RETURN PREFIX TO NEW TAXO WITHOUT CREATING ANYTHING
# The URI targets a taxonomy # The URI targets a taxonomy
# dms:dmspath/taxonomy/taxoname[/taxid] # dms:dmspath/taxonomy/taxoname[/taxid]
if path_parts[0]==b"taxonomy": if path_parts[0]==b"taxonomy":
@ -282,20 +283,20 @@ def open_uri(uri,
raise MalformedURIException('Malformed noquality argument in URI') raise MalformedURIException('Malformed noquality argument in URI')
if b"qualityformat" in qualifiers: if b"qualityformat" in qualifiers:
if qualifiers[b"qualityformat"][0]=="sanger": if qualifiers[b"qualityformat"][0]==b"sanger":
offset=33 offset=33
elif qualifiers[b"qualityformat"][0]=="solexa": elif qualifiers[b"qualityformat"][0]==b"solexa":
offset=64 offset=64
else: else:
try: try:
if config["obi"]["qualityformat"][0]=="sanger": if config["obi"]["qualityformat"]==b"sanger":
offset=33 offset=33
elif config["obi"]["qualityformat"][0]=="solexa": elif config["obi"]["qualityformat"]==b"solexa":
offset=64 offset=64
#offset=config["obi"]["offset"] # TODO discuss #offset=config["obi"]["offset"] # TODO discuss
except KeyError: except KeyError:
offset=33 offset=33
if b"header" in qualifiers: if b"header" in qualifiers:
try: try:
header=eval(qualifiers[b"header"][0]) header=eval(qualifiers[b"header"][0])