debian/changelog

+mapdamage (2.0.9+dfsg-1) unstable; urgency=medium
+
+  * New upstream version
+  * Remove trailing whitespace in debian/changelog
+  * Remove trailing whitespace in debian/rules
+
+ -- Andreas Tille <tille@debian.org>  Sat, 08 Dec 2018 22:38:50 +0100
+
 mapdamage (2.0.8+dfsg-2) unstable; urgency=medium
 
   [ Steffen Moeller ]

mapdamage/Rscripts/stats/function.R

@@ -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

@@ -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