jamescasbon

$ 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'

jamescasbon

# 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

jamescasbon

# 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("""