@@ -1,3 +1,18 @@

+CHANGES IN VERSION 1.8.0

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

+

+NEW FEATURES

+

+    o GmapGenomes can be built from any file supported by rtracklayer

+      (so 2bit now works, as well as fasta).

+

+    o Tally BAM files by codon given a set of transcript

+      structures. This happens at the read level, i.e., a codon is

+      observed within an individual read.

+

+    o Tally BAM files strand by XS tag (inferred strand of

+      transcription, instead of strand of alignment).

+    

 CHANGES IN VERSION 1.6.0

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

@@ -1,3 +1,29 @@

+CHANGES IN VERSION 1.6.0

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

+

+NEW FEATURES

+

+    o Add median distance from nearest end (MDFNE) statistics to output

+      of variantSummary.

+

+    o Updated GSNAP, which is orders of magnitude faster than the

+      previous version, brings many fixes and offers many new

+      features. One new feature is the clip_overlap argument, which

+      clips overlapping ends of read pairs (important for variant

+      calling).

+

+    o Updated bam_tally, which is faster and includes support for

+      counting in soft-clipped regions.

+    

+USER-VISIBLE CHANGES

+

+    o Changes to tallyVariant statistics: drop the unique read

+      position counts; renamed count.pos/count.neg to

+      count.plus/count.minus (way better names)

+

+    o tallyVariants does a better job of carrying over the Seqinfo

+      from the BAM file.

+    

 CHANGES IN VERSION 1.4.0

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

@@ -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

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

new file mode 100644

@@ -0,0 +1,30 @@

+CHANGES IN VERSION 1.2.0

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

+

+NEW FEATURES

+

+    o New method getSeq,GmapGenome retrieves sequence from a

+      GmapGenome index. This also supports a coercion to DNAStringSet

+      and thus easy export to FASTA via rtracklayer.

+

+    o bam_tally gains an ignore_duplicates argument for ignoring BAM

+      records flagged as PCR/optical duplicates.

+

+    o Read position mean and variance are now output by bam_tally.

+

+USER-VISIBLE CHANGES

+

+    o GMAP has been updated to the July '12 version (yes, this is old).

+    

+    o GSTRUCT (bamtally) updated to trunk as of 3/22/13.

+    

+BUG FIXES

+

+    o asBam,GsnapOutput now actually works.

+

+CHANGES IN VERSION 1.0.0

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

+

+Initial release

+

+(start date: 12 September, 2012)