X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=WHAT_IS_NEW;h=ecd93cf519e6f4d8d3e00cf6484b78c0c926f119;hp=64dc6e55768b12dc467e1909b84a964c7dab3d9a;hb=412c1a2821c5a4cbe2e68e4e9f4e2026a86d25f7;hpb=da3cf29fde8e879f83cde41831ddbc0456ba35dd

diff --git a/WHAT_IS_NEW b/WHAT_IS_NEW
index 64dc6e5..ecd93cf 100644
--- a/WHAT_IS_NEW
+++ b/WHAT_IS_NEW
@@ -1,3 +1,81 @@
+RSEM v1.2.13
+
+- Allowed users to use the SAMtools in the PATH first and enabled RSEM to find its executables via a symbolic link
+- Changed the behavior of parsing GTF file. Now if a GTF line's feature is not "exon" and it does not contain a "gene_id" or "transcript_id" attribute, only a warning message will be produced (instead of failing the RSEM)
+
+--------------------------------------------------------------------------------------------
+
+RSEM v1.2.12
+
+- Enabled allele-specific expression estimation
+- Added '--calc-pme' option for 'rsem-calculate-expression' to calculate posterior mean estimates only (no credibility intervals)
+- Modified the shebang line of RSEM perl scripts to make them more portable
+- Added '--seed' option for 'rsem-simulate-reads' to enable users set the seed of random number generator used by the simulation
+- Modified the transcript extraction behavior of 'rsem-prepare-reference'. For transcripts that cannot be extracted, instead of failing the whole script, warning information is produced. Those transcripts are ignored
+
+--------------------------------------------------------------------------------------------
+
+RSEM v1.2.11
+
+- Enabled RSEM to use Bowtie 2 aligner (indel, local and discordant alignments are not supported yet)
+- Changed option names '--bowtie-phred33-quals', '--bowtie-phred64-quals' and '--bowtie-solexa-quals' back to '--phred33-quals', '--phred64-quals' and '--solexa-quals' 
+
+--------------------------------------------------------------------------------------------
+
+RSEM v1.2.10
+
+- Fixed a bug which will lead to out-of-memory error when RSEM computes ngvector for EBSeq
+
+--------------------------------------------------------------------------------------------
+
+RSEM v1.2.9
+
+- Fixed a compilation error problem in Mac OS
+- Fixed a problem in makefile that affects 'make ebseq'
+- Added 'model_file_description.txt', which describes the format and meanings of file 'sample_name.stat/sample_name.model'
+- Updated samtools to version 0.1.19
+
+--------------------------------------------------------------------------------------------
+
+RSEM v1.2.8
+
+- Provided a more detailed description for how to simulate RNA-Seq data using 'rsem-simulate-reads'
+- Provided more user-friendly error message if RSEM fails to extract transcript sequences due to the failure of reading certain chromosome sequences
+
+--------------------------------------------------------------------------------------------
+
+RSEM v1.2.7
+
+- 'rsem-find-DE' is replaced by 'rsem-run-ebseq' and 'rsem-control-fdr' for a more friendly user experience
+- Added support for differential expression testing on more than 2 conditions in RSEM's EBSeq wrappers 'rsem-run-ebseq' and 'rsem-control-fdr'
+- Renamed '--phred33-quals', '--phred64-quals', and '--solexa-quals' in 'rsem-calculate-expression' to '--bowtie-phred33-quals', '--bowtie-phred64-quals', and '--bowtie-solex-quals' to avoid confusion
+
+--------------------------------------------------------------------------------------------
+
+RSEM v1.2.6
+
+- Install the latest version of EBSeq from Bioconductor and if fails, try to install EBSeq v1.1.5 locally
+- Fixed a bug in 'rsem-gen-transcript-plots', which makes 'rsem-plot-transcript-wiggles' fail 
+
+--------------------------------------------------------------------------------------------
+
+RSEM v1.2.5
+
+- Updated EBSeq from v1.1.5 to v1.1.6
+- Fixed a bug in 'rsem-generate-data-matrix', which can cause 'rsem-find-DE' to crash 
+
+--------------------------------------------------------------------------------------------
+
+RSEM v1.2.4
+
+- Fixed a bug that leads to poor parallelization performance in Mac OS systems
+- Fixed a problem that may halt the 'rsem-gen-transcript-plots", thanks Han Lin for pointing out the problem and suggesting possible fixes  
+- Added some user-friendly error messages for converting transcript BAM files into genomic BAM files
+- Modified rsem-tbam2gbam so that the original alignment quality MAPQ will be preserved if the input bam is not from RSEM
+- Added user-friendly error messages if users forget to compile the source codes
+
+--------------------------------------------------------------------------------------------
+
 RSEM v1.2.3
 
 - Fixed a bug in 'EBSeq/rsem-for-ebseq-generate-ngvector-from-clustering-info' which may crash the script