[med-svn] [Git][med-team/mapdamage][upstream] New upstream version 2.0.9+dfsg

[Andreas Tille]

Andreas Tille pushed to branch upstream at Debian Med / mapdamage


Commits:
4ae67b6e by Andreas Tille at 2018-12-08T21:38:12Z
New upstream version 2.0.9+dfsg
- - - - -


2 changed files:

- mapdamage/Rscripts/stats/function.R
- mapdamage/seq.py


Changes:

=====================================
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
 
 



View it on GitLab: https://salsa.debian.org/med-team/mapdamage/commit/4ae67b6e366edb1deff9061947c4a08f3e8def5d

-- 
View it on GitLab: https://salsa.debian.org/med-team/mapdamage/commit/4ae67b6e366edb1deff9061947c4a08f3e8def5d
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