@@ -5,6 +5,7 @@ SIGNIFICANT USER-VISIBLE CHANGES

     o Provide interval-level likelihood scores in runAbsoluteCN return

       object. Thanks @tinyheero (#335).

+    o Documentation updates. Thanks @ddrichel (#325).  

 BUGFIXES

@@ -223,7 +223,7 @@ interval.padding = 50, DB.info.flag = "DB") {

     }

     if (!is.null(info(vcf)[[DB.info.flag]]) &&

         sum(info(vcf)[[DB.info.flag]]) < nrow(vcf) / 2) {

-        flog.warn("Less than half of variants are likely somatic. Make sure that VCF %s",

+        flog.warn("Less than half of variants are annoted as germline database member. Make sure that VCF %s",

             "contains both germline and somatic variants.")

     }

@@ -523,7 +523,7 @@ function(vcf, tumor.id.in.vcf, allowed = 0.05) {

     newInfo <- DataFrame(

         Number = 0,

         Type = "Flag",

-        Description = "Likely somatic status, based on SOMATIC or Cosmic.CNT info fields, population allele frequency, or dbSNP membership",

+        Description = "Likely somatic status, based on SOMATIC or Cosmic.CNT info fields, population allele frequency, or germline database membership",

         row.names = DB.info.flag)

     info(header(vcf)) <- rbind(info(header(vcf)), newInfo)

     info(vcf)[[DB.info.flag]] <- db

@@ -80,7 +80,7 @@ readAllelicCountsFile <- function(file, format, zero=NULL) {

     info(header(vcf)) <- DataFrame(

         Number = "0",

         Type = "Flag",

-        Description = "Likely somatic status, based on SOMATIC or Cosmic.CNT info fields, population allele frequency, or dbSNP membership",

+        Description = "Likely somatic status, based on SOMATIC or Cosmic.CNT info fields, population allele frequency, or germline database membership",

         row.names = "DB")

     geno(header(vcf)) <- DataFrame(

@@ -29,7 +29,7 @@

 #' @param vcf.file VCF file.

 #' Optional, but typically needed to select between local optima of similar

 #' likelihood. Can also be a \code{CollapsedVCF}, read with the \code{readVcf}

-#' function.  Requires a DB info flag for likely somatic status. The default

+#' function.  Requires a DB info flag for likely germline status. The default

 #' \code{fun.setPriorVcf} function will also look for a Cosmic.CNT slot (see

 #' \code{cosmic.vcf.file}), containing the hits in the COSMIC database. Again,

 #' do not expect very useful results without a VCF file.

@@ -60,14 +60,14 @@ setPriorVcf <- function(vcf, prior.somatic = c(0.5, 0.0005, 0.999, 0.0001,

          if (!is.null(info(vcf)[[Cosmic.CNT.info.field]])) {

              flog.info("Found COSMIC annotation in VCF. Requiring %i hits.", 

                 min.cosmic.cnt)

-             flog.info("Setting somatic prior probabilities for hits to %f or to %f if in both COSMIC and likely somatic based on dbSNP membership or population allele frequency.", 

+             flog.info("Setting somatic prior probabilities for hits to %f or to %f if in both COSMIC and likely germline based on dbSNP membership or population allele frequency.", 

                 tmp[5], tmp[6])

              prior.somatic[which(info(vcf)[[Cosmic.CNT.info.field]] >= min.cosmic.cnt)] <- tmp[5]

              prior.somatic[which(info(vcf)[[Cosmic.CNT.info.field]] >= min.cosmic.cnt & 

                 info(vcf)[[DB.info.flag]])] <- tmp[6]

          } else {

-             flog.info("Setting somatic prior probabilities for likely somatic hits to %f or to %f otherwise.", 

+             flog.info("Setting somatic prior probabilities for likely germline hits to %f or to %f otherwise.", 

                 tmp[2], tmp[1])

          }      

     }     

@@ -105,7 +105,7 @@ option_list <- list(

         help = "Maximum considered ploidy [default %default]"),

     make_option(c("--max-copy-number"), action = "store", type = "double",

         default =  max(eval(formals(PureCN::runAbsoluteCN)$test.num.copy)),

-        help = "Maximum allele-specific integer copy number, only used for fitting allele-specific copy numbers. Higher copy numbers might still be inferred and reported [default %default]"),

+        help = "Maximum allele-specific integer copy number, only used for fitting allele-specific copy numbers. Higher copy numbers are still be inferred and reported [default %default]"),

     make_option(c("--post-optimize"), action = "store_true", default = FALSE,

         help = "Post-optimization [default %default]"),

     make_option(c("--bootstrap-n"), action = "store", type = "integer", default = 0,

@@ -7,9 +7,9 @@

 filterVcfMuTect2(

   vcf,

   tumor.id.in.vcf = NULL,

-  ignore = c("clustered_events", "t_lod", "str_contraction", "read_position", "position",

-    "fragment_length", "multiallelic", "clipping", "strand_artifact", "strand_bias",

-    "slippage", "weak_evidence", "orientation", "haplotype"),

+  ignore = c("clustered_events", "t_lod", "str_contraction", "read_position",

+    "position", "fragment_length", "multiallelic", "clipping", "strand_artifact",

+    "strand_bias", "slippage", "weak_evidence", "orientation", "haplotype"),

   ...

 )

 }

@@ -98,7 +98,7 @@ deviation, used to model likelihood of sub-clonal copy number events.}

 \item{vcf.file}{VCF file.

 Optional, but typically needed to select between local optima of similar

 likelihood. Can also be a \code{CollapsedVCF}, read with the \code{readVcf}

-function.  Requires a DB info flag for likely somatic status. The default

+function.  Requires a DB info flag for likely germline status. The default

 \code{fun.setPriorVcf} function will also look for a Cosmic.CNT slot (see

 \code{cosmic.vcf.file}), containing the hits in the COSMIC database. Again,

 do not expect very useful results without a VCF file.}