Merge pull request #63 from timbitz/bfs-bugfix

Some default value updates for v0.10.2

Author: Tim Sterne-Weiler

bin/VERSION

@@ -1 +1 @@
-v0.10.1
+v0.10.2

bin/whippet-quant.jl

@@ -67,7 +67,7 @@ function parse_cmd()
     "--score-min", "-S"
       help     = "Minimum percent matching (matches - mismatches) / read_length"
       arg_type = Float64
-      default  = 0.6
+      default  = 0.7
     "--psi-body-read"
       help     = "Allow exon-body reads in quantification of PSI values"
       action   = :store_true

src/events.jl

@@ -644,7 +644,7 @@ end
 
 function _process_spliced( sg::SpliceGraph, sgquant::SpliceGraphQuant, 
                            node::NodeInt, motif::EdgeMotif, bias::Float64, isnodeok::Bool,
-                           minedgeweight::Float64=0.025 )
+                           minedgeweight::Float64=0.02 )
 
    inc_graph  = Nullable{PsiGraph}()
    exc_graph  = Nullable{PsiGraph}()

src/quant.jl

@@ -6,16 +6,12 @@ const SCALING_FACTOR = 1_000_000
 # overridden for more complex count bias models
 #const ReadCount = JointBiasCounter #DefaultCounter
 const DEFAULT_DEF   = (v = zero(DefaultCounter); v.isadjusted = true; v)
-#const DEFAULT_PRIME = (v = zero(PrimerBiasCounter); v.isadjusted = true; v)
-#const DEFAULT_GC    = (v = zero(GCBiasCounter); v.isadjusted = true; v)
 const DEFAULT_JOINT = (v = zero(JointBiasCounter); v.isadjusted = true; v)
 
 const DEF_READCOUNT = 0.0
 const DEF_READVALUE = 1.0
 
 default(::Type{DefaultCounter}) = DEFAULT_DEF
-#default(::Type{PrimerBiasCounter}) = DEFAULT_PRIME
-#default(::Type{GCBiasCounter}) = DEFAULT_GC
 default(::Type{JointBiasCounter}) = DEFAULT_JOINT
 
 # Use this abstraction to store SGAlignPaths before

src/refset.jl

@@ -14,8 +14,6 @@ struct RefGene
    acc::CoordTuple 
    txst::CoordTuple
    txen::CoordTuple
-#   orfst::CoordTuple
-#   orfen::CoordTuple
    exons::CoordTree
    length::Float64
    reftx::Vector{RefTx}
@@ -55,8 +53,6 @@ function load_refflat( fh; txbool=true )
    gnacc    = Dict{GeneName,CoordTuple}()
    gntxst   = Dict{GeneName,CoordTuple}()
    gntxen   = Dict{GeneName,CoordTuple}()
-#   gnorfst  = Dict{GeneName,CoordTuple}()
-#   gnorfen  = Dict{GeneName,CoordTuple}()
    gnlens   = Dict{GeneName,CoordTuple}()
    gnexons  = Dict{GeneName,CoordTree}()
    gnreftx  = Dict{GeneName,Vector{RefTx}}()
@@ -163,8 +159,6 @@ function load_gtf( fh; txbool=true, suppress=false )
    gnacc    = Dict{GeneName,CoordTuple}()
    gntxst   = Dict{GeneName,CoordTuple}()
    gntxen   = Dict{GeneName,CoordTuple}()
- #  gnorfst  = Dict{GeneName,CoordTuple}()
- #  gnorfen  = Dict{GeneName,CoordTuple}()
    gnlens   = Dict{GeneName,CoordTuple}()
    gnexons  = Dict{GeneName,CoordTree}()
    gnreftx  = Dict{GeneName,Vector{RefTx}}()
@@ -240,13 +234,13 @@ function load_gtf( fh; txbool=true, suppress=false )
       support,val = fetch_meta( "transcript_support_level", metaspl )
 
       # if we observe low transcript support levels, we will warn the user
-      if (support != "_" && support != "1" &&  support != "NA")
+      if (support != "_" && support != "1" && support != "2" &&  support != "NA")
 
          if suppress
             continue
          elseif !warning
             println(STDERR, "")
-            warn("Using low quality Transcript Support Levels (TSL 2-5) in your GTF file is not recommended!\nFor more information on TSL, see: http://www.ensembl.org/Help/Glossary?id=492\n\nIf you would like Whippet to ignore these when building its index, use `--suppress-low-tsl` option!\n\n")
+            warn("Using low quality Transcript Support Levels (TSL 3+) in your GTF file is not recommended!\nFor more information on TSL, see: http://www.ensembl.org/Help/Glossary?id=492\n\nIf you would like Whippet to ignore these when building its index, use `--suppress-low-tsl` option!\n\n")
 
             warning=true
          end