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$ make | |
cd ../bamtools && mkdir -p build && cd build && cmake .. && make | |
-- Configuring done | |
-- Generating done | |
-- Build files have been written to: /home/james/src/freebayes/bamtools/build | |
make[1]: Entering directory `/home/james/src/freebayes/bamtools/build' | |
make[2]: Entering directory `/home/james/src/freebayes/bamtools/build' | |
make[3]: Entering directory `/home/james/src/freebayes/bamtools/build' | |
make[3]: Leaving directory `/home/james/src/freebayes/bamtools/build' | |
make[3]: Entering directory `/home/james/src/freebayes/bamtools/build' |
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# quickly fix mapping qualities in samfiles generated by SSAHA2 | |
# mapq 255 is undefined according to spec, but SSAHA2 is not | |
# following this convention | |
import pysam | |
infile = pysam.Samfile( "-", "rb" ) | |
outfile = pysam.Samfile( "-", "wb", template = infile ) | |
for s in infile: | |
if s.mapq == 255: | |
s.mapq = 244 |
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# hmm no imports ;) | |
class BaseHandler(cyclone.web.RequestHandler): | |
def get_current_user(self): | |
return self.get_secure_cookie("user") | |
class LoginHandler(BaseHandler): | |
def get(self): | |
err = self.get_argument("e", None) | |
self.finish(""" |
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