From: Don Armstrong <don@donarmstrong.com>
Date: Mon, 29 Sep 2014 18:04:17 +0000 (-0700)
Subject: Imported Upstream version 1.2.17
X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=commitdiff_plain;h=abfbe423f2db1399c067e4a3b043cf1217702336

Imported Upstream version 1.2.17
---

diff --git a/.gitignore b/.gitignore
deleted file mode 100644
index 794b993..0000000
--- a/.gitignore
+++ /dev/null
@@ -1,20 +0,0 @@
-*.o
-*.a
-*~
-rsem-bam2readdepth
-rsem-bam2wig
-rsem-build-read-index
-rsem-calculate-credibility-intervals
-rsem-extract-reference-transcripts
-rsem-get-unique
-rsem-parse-alignments
-rsem-preref
-rsem-run-em
-rsem-run-gibbs
-rsem-simulate-reads
-rsem-synthesis-reference-transcripts
-rsem-tbam2gbam
-rsem-sam-validator
-rsem-scan-for-paired-end-reads
-EBSeq/rsem-for-ebseq-calculate-clustering-info
-sam/samtools
diff --git a/WHAT_IS_NEW b/WHAT_IS_NEW
index e9def23..76643c5 100644
--- a/WHAT_IS_NEW
+++ b/WHAT_IS_NEW
@@ -1,3 +1,9 @@
+RSEM v1.2.17
+
+- Added error detection for cases such as a read's two mates having different names or a read is both alignable and unalignable
+
+--------------------------------------------------------------------------------------------
+
 RSEM v1.2.16
 
 - Corrected a typo in 'rsem-generate-data-matrix', this script extracts 'expected_count' column instead of 'TPM' column