Commit 4ae67b6e authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 2.0.9+dfsg

parent d046a9d5

mapdamage/Rscripts/stats/function.R

+2 −2
Original line number Diff line number Diff line
@@ -145,7 +145,7 @@ seqProbVecLambda <- function(lambda,lambda_disp,m,fo_only=NA,re_only=NA){ 


#The following is an MC simulation code to mimic the 

#nick frequency part in the model from Philip

seqProbVecNuWithLengths<- cxxfunction( signature(

seqProbVecNuWithLengths<- cxxfunction(methods::signature(

                                      I_la="numeric",

                                      I_la_disp="numeric",

                                      I_nu="numeric",
@@ -270,7 +270,7 @@ logLikFunOneBaseSlow <- function(Gen,S,Theta,deltad,deltas,laVec,nuVec,m,lin){ 


#The same logic as in logLikFunOneBaseSlow except using a compiled code 

#to do the hard work

logLikFunOneBaseFast <- cxxfunction(signature(

logLikFunOneBaseFast <- cxxfunction(methods::signature(

                                      I_Gen="numeric",

                                      I_S="numeric",

                                      I_Theta="numeric",

mapdamage/seq.py

+6 −0
Original line number Diff line number Diff line
@@ -63,6 +63,12 @@ def read_fasta_index(filename): 
        print_err("Column 2 in FASTA index did not contain a number, found '%s':" % ref[1], filename, line)

        return None



  if not fai:

    sys.stderr.write("Error: Index for %r does contain any sequences.\n" % (filename,))

    sys.stderr.write("       Please ensure that FASTA file is valid, and\n")

    sys.stderr.write("       re-index file using 'samtool faidx'.\n")

    return None



  return fai