@@ -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

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