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2014-06-08	Bo Li	For genome BAM, modified MD tag accordingly	commit \| commitdiff \| tree
2014-06-08	Bo Li	Renamed makefile as Makefile	commit \| commitdiff \| tree
2014-06-06	Bo Li	Modified the use of uniform_01	commit \| commitdiff \| tree
2014-06-06	Bo Li	Added posterior standard deviation of counts as output...	commit \| commitdiff \| tree
2014-06-06	Bo Li	Added --seed option to set random number generator...	commit \| commitdiff \| tree
2014-06-05	Bo Li	Modified RSEM perl scripts so that RSEM directory will...	commit \| commitdiff \| tree
2014-06-05	Bo Li	Removed '--no-bowtie' and '--no-ntog' options in 'rsem...	commit \| commitdiff \| tree
2014-06-05	Bo Li	Generated two index multi-Fasta files instead, one...	commit \| commitdiff \| tree
2014-05-27	Bo Li	WHAT_IS_NEW is updated	commit \| commitdiff \| tree
2014-05-27	Bo Li	Changed the behavior of parsing GTF file. Now if a...	commit \| commitdiff \| tree
2014-04-03	Bo Li	Use PATH env to instead the variable	commit \| commitdiff \| tree
2014-03-27	Bo Li	Modified the acknowledgement section of README.md	commit \| commitdiff \| tree
2014-03-27	Bo Li	Modified the transcript extraction behavior of 'rsem...	commit \| commitdiff \| tree
2014-03-22	Bo Li	Added '--seed' option for 'rsem-simulate-reads'	commit \| commitdiff \| tree
2014-03-21	Bo Li	Modified the shebang line for perl scripts	commit \| commitdiff \| tree
2014-03-21	Bo Li	Added support for allele-specific expression estimation	commit \| commitdiff \| tree
2014-03-09	Bo Li	Fixed a typo in rsem-calculate-expression's document...	commit \| commitdiff \| tree
2014-02-14	Bo Li	Added Bowtie 2 support	commit \| commitdiff \| tree
2014-02-01	Bo Li	Fixed a bug which will lead to out-of-memory error...	commit \| commitdiff \| tree
2014-01-11	Bo Li	Removed unnecessary spaces in POD doc of rsem-calculate...	commit \| commitdiff \| tree
2014-01-09	Bo Li	Added update samtools to WHAT_IS_NEW	commit \| commitdiff \| tree
2014-01-09	Bo Li	Modified WHAT_IS_NEW for RSEM v1.2.9	commit \| commitdiff \| tree
2014-01-09	Bo Li	Fixed a problem that will lead compilation errors for...	commit \| commitdiff \| tree
2014-01-09	Bo Li	README.md is updated	commit \| commitdiff \| tree
2014-01-09	Bo Li	Updated samtools to 0.1.19	commit \| commitdiff \| tree
2013-12-02	Bo Li	Added a file describing the format of sample_name.stat...	commit \| commitdiff \| tree
2013-11-22	Bo Li	Provided a more detailed description for how to simulate...	commit \| commitdiff \| tree
2013-09-25	Bo Li	Added a line in WHAT_IS_NEW for renaming of quality...	commit \| commitdiff \| tree
2013-09-07	Bo Li	Fixed a displaying problem for rsem-run-ebseq's Pod...	commit \| commitdiff \| tree
2013-09-07	Bo Li	Fixed loading library problem for EBSeq/install	commit \| commitdiff \| tree
2013-09-07	Bo Li	Fixed a bug for adding EBSeq's local library path	commit \| commitdiff \| tree
2013-09-07	Bo Li	Changed WHAT_IS_NEW	commit \| commitdiff \| tree
2013-09-07	Bo Li	'rsem-run-ebseq': Added 'output_file.condmeans' for...	commit \| commitdiff \| tree
2013-09-02	Bo Li	Added support for DE analysis on multiple conditions...	commit \| commitdiff \| tree
2013-08-28	Bo Li	Renamed --phred33-quals, --phred64-quals, and --solexa...	commit \| commitdiff \| tree
2013-08-21	Bo Li	Fixed a minor bug which only affects paired-end reads...	commit \| commitdiff \| tree
2013-07-31	Bo Li	Install the latest version of EBSeq from Bioconductor...	commit \| commitdiff \| tree
2013-07-04	Bo Li	Fixed a bug in rsem-find-DE, which will crash the script...	commit \| commitdiff \| tree
2013-06-26	Bo Li	Updated EBSeq from v1.1.5 to v1.1.6 and fixed a bug...	commit \| commitdiff \| tree
2013-04-15	Bo Li	Modifed README.md and WHAT_IS_NEW	commit \| commitdiff \| tree
2013-04-15	Bo Li	Modified wiggle.cpp & wiggle.h for more accurate floating...	commit \| commitdiff \| tree
2013-04-15	Bo Li	Modified my_assert.h to postpone error message string...	commit \| commitdiff \| tree
2013-04-05	Bo Li	Removed a too stringent sanity check in rsem-gen-transcript...	commit \| commitdiff \| tree
2013-03-27	Bo Li	remove .gitignore from the staging area	commit \| commitdiff \| tree
2013-03-22	Bo Li	Added some user-friendly error messages for BamConverter.h	commit \| commitdiff \| tree
2013-03-22	Bo Li	Modified rsem-tbam2gbam so that the original alignment...	commit \| commitdiff \| tree
2013-01-27	Bo Li	Fixed a bug that will lead perl scripts fail to find...	commit \| commitdiff \| tree
2013-01-24	Bo Li	Added user-friendly error messages if users forget...	commit \| commitdiff \| tree
2013-01-08	Bo Li	Fixed a bug in 'EBSeq/rsem-for-ebseq-generate-ngvector...	commit \| commitdiff \| tree
2013-01-07	Bo Li	Modified rsem-find-DE	commit \| commitdiff \| tree
2013-01-07	Bo Li	Updated EBSeq to v1.1.5	commit \| commitdiff \| tree
2012-11-30	Bo Li	- Added poly(A) tails to 'reference_name.transcripts...	commit \| commitdiff \| tree
2012-10-21	Bo Li	Updated EBSeq to v1.1.4	commit \| commitdiff \| tree
2012-10-18	Bo Li	Added --version option for rsem-calculate-expression	commit \| commitdiff \| tree
2012-10-10	Bo Li	use if/elsif to replace switch in rsem-calculate-expression	commit \| commitdiff \| tree
2012-09-24	Bo Li	Fixed a bug to make RSEM generated BAM file valid input...	commit \| commitdiff \| tree
2012-09-15	Bo Li	If a gene is not expressed, its length/effective length...	commit \| commitdiff \| tree
2012-09-11	Bo Li	README.md is changed	commit \| commitdiff \| tree
2012-09-11	Bo Li	Added a script, 'rsem-find-DE', to run EBSeq automatically	commit \| commitdiff \| tree
2012-09-10	Bo Li	changed output format to contain FPKM etc. ; fixed...	commit \| commitdiff \| tree
2012-07-27	Bo Li	Added a user-friendly error message for rsem-sam-validator	commit \| commitdiff \| tree
2012-07-23	Bo Li	Fixed a bug for calling pthread_join	commit \| commitdiff \| tree
2012-07-22	Bo Li	Fixed a bug in perl scripts for printing error messages	commit \| commitdiff \| tree
2012-07-15	Bo Li	Fix a bug on convert-sam-for-rsem for the case that...	commit \| commitdiff \| tree
2012-07-02	Bo Li	rsem v1.1.21	commit \| commitdiff \| tree
2012-06-06	Bo Li	Tested the codes	commit \| commitdiff \| tree
2012-06-05	Bo Li	Made the BAM output of RSEM have all information contained...	commit \| commitdiff \| tree
2012-04-26	Bo Li	Included EBSeq for downstream differential expression...	commit \| commitdiff \| tree
2012-04-15	Bo Li	Added some instructions on how to visualize transcript...	commit \| commitdiff \| tree
2012-04-14	Bo Li	Fixed a bug related to intermediate output displaying...	commit \| commitdiff \| tree
2012-04-14	Bo Li	Fixed a bug related to intermediate output displaying...	commit \| commitdiff \| tree
2012-03-21	Bo Li	Allowed > 2^31 hits	commit \| commitdiff \| tree
2012-03-11	Bo Li	Modified makefile to work for gcc version 4.5.3 or...	commit \| commitdiff \| tree
2012-03-11	Bo Li	Modified 'convert-sam-for-rsem' so that this program...	commit \| commitdiff \| tree
2012-03-11	Bo Li	Add a validator for input SAM/BAM file	commit \| commitdiff \| tree
2012-03-09	Bo Li	Improved warning messages in rsem-gen-transcript-plots	commit \| commitdiff \| tree
2012-03-09	Bo Li	Add warning messages for detected invalid alignments	commit \| commitdiff \| tree
2012-02-19	Bo Li	[Change] Do not add --phred33-qual option if --no-qualities...	commit \| commitdiff \| tree
2012-02-09	Bo Li	The order of @SQ tags in SAM/BAM files can be arbitrary now	commit \| commitdiff \| tree
2012-02-08	Bo Li	add --no-bam-output option to not generate output bam...	commit \| commitdiff \| tree
2012-02-08	Bo Li	roll back to original version plus fixed a small bug...	commit \| commitdiff \| tree
2012-02-08	Bo Li	rewrote parallelization of calcCI.cpp	commit \| commitdiff \| tree
2012-01-31	Bo Li	rsem v1.1.16	commit \| commitdiff \| tree
2012-01-26	Bo Li	rsem v1.1.15	commit \| commitdiff \| tree
2012-01-18	Bo Li	rsem v1.1.14	commit \| commitdiff \| tree
2011-12-31	Bo Li	relax the requirement about GTF attribute format	commit \| commitdiff \| tree
2011-12-14	Bo Li	modify one error message and add --bowtie-chunkmbs...	commit \| commitdiff \| tree
2011-12-14	Bo Li	Merge remote-tracking branch 'origin/master'	commit \| commitdiff \| tree
2011-12-14	Bo Li	another change	commit \| commitdiff \| tree
2011-12-14	bli25wisc	Merge pull request #1 from earonesty/master	commit \| commitdiff \| tree
2011-12-10	Bo Li	updated some description	commit \| commitdiff \| tree
2011-12-10	Bo Li	new update	commit \| commitdiff \| tree
2011-12-09	Bo Li	convert-sam-for-rsem is updated	commit \| commitdiff \| tree
2011-12-09	Bo Li	add a script to convert sam file for non-bowtie aligner	commit \| commitdiff \| tree
2011-12-04	Bo Li	rsem-v1.1.14b3	commit \| commitdiff \| tree
2011-12-02	Bo Li	rsem-1.1.14 with transcript wiggle plot generation	commit \| commitdiff \| tree
2011-12-01	Bo Li	add new files	commit \| commitdiff \| tree
2011-11-28	Bo Li	tested version for tbam2gbam	commit \| commitdiff \| tree
2011-11-11	Bo Li	some displaying issue in rsem-calculate-expression...	commit \| commitdiff \| tree
2011-11-11	Bo Li	add optional field XS for cufflinks	commit \| commitdiff \| tree
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