@@ -10,13 +10,13 @@ Description: GSNAP and GMAP are a pair of tools to align short-read

     to work with GMAP and GSNAP from within R. In addition, it provides 

     methods to tally alignment results on a per-nucleotide basis using 

     the bam_tally tool.

-Version: 1.5.0

+Version: 1.5.1

 Depends: R (>= 2.15.0), methods, GenomicRanges

-Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15), GenomicRanges,

-         GenomicFeatures, Biostrings, VariantAnnotation (>= 1.7.34), tools,

-         Biobase, BSgenome, methods

+Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),

+         GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4), tools,

+         Biobase, BSgenome

 Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3,

-	  BSgenome.Scerevisiae.UCSC.sacCer3, VariantAnnotation,

+	  BSgenome.Scerevisiae.UCSC.sacCer3,

           org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene,

           BSgenome.Hsapiens.UCSC.hg19, LungCancerLines

 License: Artistic-2.0

@@ -1,3 +1,44 @@

+CHANGES IN VERSION 1.4.0

+-----------------------

+

+NEW FEATURES

+

+    o Add desired_read_group to BamTallyParam; will limit tallies to

+      that specific read group (useful for multi-amplicon sequencing,

+      like Fluidigm)

+

+    o Add keep_ref_rows argument to variantSummary() for keeping rows

+      for positions where no alt is detected (the rows where ref == alt).

+

+    o gsnap() will now output a GsnapOutputList when there are

+      multiple input files

+

+    o Support 'terminal_threshold' and 'gmap_mode' parameters in

+      GsnapParam, and use different defaults for DNA vs. RNA. This

+      means a big improvement in alignment quality for DNA.

+

+    o GmapGenome now accepts a direct path to the genome as its first argument

+    

+USER-VISIBLE CHANGES

+

+    o Renamed summarizeVariants to variantSummary

+

+    o The 'which' in GsnapParam is now a GenomicRanges instead of a RangesList

+

+    o Refactor bam_tally, so that bam_tally returns a TallyIIT object,

+      which is then summarized via summarizeVariants; this allows computing

+      tallies once and summarizing them in different ways (like maybe get

+      the coverage). The summarizeVariants function yields a VRanges.

+

+BUG FIXES

+

+    o fix minimum quality cutoff check to >=, instead of >

+

+    o fix asBam,GsnapOutput for when unique_only is TRUE

+

+    o package created by makeGmapGenomePackage now have a GmapGenome with

+      the correct name

+

 CHANGES IN VERSION 1.2.0

 -----------------------

@@ -82,6 +82,7 @@ variantSummary <- function(x, read_pos_breaks = NULL, high_base_quality = 0L,

                    "count.neg", "count.neg.ref",

                    "read.pos.mean", "read.pos.mean.ref",

                    "read.pos.var", "read.pos.var.ref")

+  break_names <- character()

   if (length(read_pos_breaks) > 0L) {

     read_pos_breaks <- as.integer(read_pos_breaks)

     break_names <- paste("readPosCount", head(read_pos_breaks, -1),

@@ -101,6 +102,8 @@ variantSummary <- function(x, read_pos_breaks = NULL, high_base_quality = 0L,

                           "high.quality.ref", "high.quality.total"))

   genome <- genome(x)

   indel <- nchar(tally$ref) == 0L | nchar(tally$alt) == 0L

+  metacols <- DataFrame(tally[meta_names])

+  mcols(metacols) <- variantSummaryColumnDescriptions(read_pos_breaks)

   gr <- with(tally,

              VRanges(seqnames,

                      IRanges(pos,

@@ -109,8 +112,8 @@ variantSummary <- function(x, read_pos_breaks = NULL, high_base_quality = 0L,

                      ifelse(indel, raw.count.total, high.quality.total),

                      ifelse(indel, raw.count.ref, high.quality.ref),

                      ifelse(indel, raw.count, high.quality),

-                     DataFrame(tally[meta_names]),

                      seqlengths = seqlengths(genome)))

+  mcols(gr) <- metacols

   seqinfo(gr) <- seqinfo(genome)

   gr <- normalizeIndelAlleles(gr, genome)

   gr

@@ -197,3 +200,33 @@ normArgTRUEorFALSE <- function(x) {

         normArgSingleInteger(blocksize),

         normArgTRUEorFALSE(verbosep))

 }

+

+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

+### Column metadata

+###

+

+variantSummaryColumnDescriptions <- function(read_pos_breaks) {

+  desc <- c(

+    n.read.pos = "Number of unique read positions for the ALT",

+    n.read.pos.ref = "Number of unique read positions for the REF",

+    raw.count = "Raw ALT count",

+    raw.count.ref = "Raw REF count",

+    raw.count.total = "Raw total count",

+    mean.quality = "Average ALT base quality",

+    mean.quality.ref = "Average REF base quality",

+    count.pos = "Raw positive strand ALT count",

+    count.pos.ref = "Raw positive strand REF count",

+    count.neg = "Raw negative strand ALT count",

+    count.neg.ref = "Raw negative strand REF count",

+    read.pos.mean = "Average read position for the ALT",

+    read.pos.mean.ref = "Average read position for the ALT",

+    read.pos.var = "Variance in read position for the ALT",

+    read.pos.var.ref = "Variance in read position for the REF")

+  if (length(read_pos_breaks) > 0L) {

+    break_desc <- paste0("Raw ALT count in read position range [",

+                         head(read_pos_breaks, -1), ",",

+                         tail(read_pos_breaks, -1), ")")

+    desc <- c(desc, break_desc)

+  }

+  DataFrame(Description = desc)

+}