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git.donarmstrong.com Git - rsem.git/log
Bo Li [Fri, 6 Jun 2014 10:41:46 +0000 (05:41 -0500)]
Modified the use of uniform_01
Bo Li [Fri, 6 Jun 2014 09:15:18 +0000 (02:15 -0700)]
Updated boost to v1.55.0
Bo Li [Fri, 6 Jun 2014 08:50:21 +0000 (03:50 -0500)]
Added posterior standard deviation of counts as output if either '--calc-pme' or '--calc-ci' is set
Bo Li [Fri, 6 Jun 2014 03:53:28 +0000 (22:53 -0500)]
Added --seed option to set random number generator seeds in 'rsem-calculate-expression'
Bo Li [Thu, 5 Jun 2014 19:46:52 +0000 (14:46 -0500)]
Modified RSEM perl scripts so that RSEM directory will be added in the beginning of PATH variable
Bo Li [Thu, 5 Jun 2014 08:58:43 +0000 (03:58 -0500)]
Removed '--no-bowtie' and '--no-ntog' options in 'rsem-prepare-reference' and put only raw extracted sequences in 'reference_name.transcripts.fa'
Bo Li [Thu, 5 Jun 2014 07:20:01 +0000 (02:20 -0500)]
Generated two index multi-Fasta files instead, one without 'N' converted to 'G' and one with 'N' converted to 'G'.
Bo Li [Tue, 27 May 2014 01:28:00 +0000 (20:28 -0500)]
WHAT_IS_NEW is updated
Bo Li [Tue, 27 May 2014 01:06:54 +0000 (20:06 -0500)]
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)
Bo Li [Thu, 3 Apr 2014 17:30:24 +0000 (12:30 -0500)]
Use PATH env to instead the variable
Bo Li [Thu, 27 Mar 2014 23:33:05 +0000 (18:33 -0500)]
Modified the acknowledgement section of README.md
Bo Li [Thu, 27 Mar 2014 23:07:42 +0000 (18:07 -0500)]
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
Bo Li [Sat, 22 Mar 2014 04:53:57 +0000 (23:53 -0500)]
Added '--seed' option for 'rsem-simulate-reads'
Bo Li [Fri, 21 Mar 2014 20:05:03 +0000 (15:05 -0500)]
Modified the shebang line for perl scripts
Bo Li [Fri, 21 Mar 2014 16:27:31 +0000 (11:27 -0500)]
Added support for allele-specific expression estimation
Bo Li [Sun, 9 Mar 2014 20:40:25 +0000 (15:40 -0500)]
Fixed a typo in rsem-calculate-expression's document; Added multi-thread and memory options to samtools sort thanks to Dr. Samuel Arvidsson
Bo Li [Fri, 14 Feb 2014 15:26:47 +0000 (09:26 -0600)]
Added Bowtie 2 support
Bo Li [Sat, 1 Feb 2014 00:03:52 +0000 (18:03 -0600)]
Fixed a bug which will lead to out-of-memory error when RSEM computes ngvector for EBSeq
Bo Li [Sat, 11 Jan 2014 20:17:32 +0000 (14:17 -0600)]
Removed unnecessary spaces in POD doc of rsem-calculate-expression'
Bo Li [Thu, 9 Jan 2014 06:32:54 +0000 (00:32 -0600)]
Added update samtools to WHAT_IS_NEW
Bo Li [Thu, 9 Jan 2014 05:55:49 +0000 (23:55 -0600)]
Modified WHAT_IS_NEW for RSEM v1.2.9
Bo Li [Thu, 9 Jan 2014 00:56:45 +0000 (18:56 -0600)]
Fixed a problem that will lead compilation errors for Mac OS
Bo Li [Thu, 9 Jan 2014 00:45:35 +0000 (18:45 -0600)]
README.md is updated
Bo Li [Thu, 9 Jan 2014 00:26:18 +0000 (18:26 -0600)]
Updated samtools to 0.1.19
Bo Li [Mon, 2 Dec 2013 07:10:41 +0000 (01:10 -0600)]
Added a file describing the format of sample_name.stat/sample_name.model
Bo Li [Fri, 22 Nov 2013 12:06:00 +0000 (06:06 -0600)]
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
Bo Li [Wed, 25 Sep 2013 18:10:40 +0000 (13:10 -0500)]
Added a line in WHAT_IS_NEW for renaming of quality score related options in 'rsem-calculate-expression'
Bo Li [Sat, 7 Sep 2013 10:52:33 +0000 (05:52 -0500)]
Fixed a displaying problem for rsem-run-ebseq's Pod document
Bo Li [Sat, 7 Sep 2013 10:38:50 +0000 (05:38 -0500)]
Fixed loading library problem for EBSeq/install
Bo Li [Sat, 7 Sep 2013 10:19:35 +0000 (05:19 -0500)]
Fixed a bug for adding EBSeq's local library path
Bo Li [Sat, 7 Sep 2013 09:54:33 +0000 (04:54 -0500)]
Changed WHAT_IS_NEW
Bo Li [Sat, 7 Sep 2013 04:00:12 +0000 (23:00 -0500)]
'rsem-run-ebseq': Added 'output_file.condmeans' for tests with more than 2 conditions
Bo Li [Mon, 2 Sep 2013 08:25:23 +0000 (03:25 -0500)]
Added support for DE analysis on multiple conditions via running EBSeq
Bo Li [Wed, 28 Aug 2013 22:11:30 +0000 (17:11 -0500)]
Renamed --phred33-quals, --phred64-quals, and --solexa-quals to --bowtie-phred33-quals, --bowtie-phred64-quals, and --bowtie-solex-quals to avoid confusion
Bo Li [Wed, 21 Aug 2013 18:07:52 +0000 (13:07 -0500)]
Fixed a minor bug which only affects paired-end reads for reporting how many alignments are processed when RSEM generates BAM outputs
Bo Li [Wed, 31 Jul 2013 07:19:15 +0000 (02:19 -0500)]
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
Bo Li [Thu, 4 Jul 2013 07:11:18 +0000 (02:11 -0500)]
Fixed a bug in rsem-find-DE, which will crash the script if only one DE gene/isoform is found
Bo Li [Wed, 26 Jun 2013 22:28:09 +0000 (17:28 -0500)]
Updated EBSeq from v1.1.5 to v1.1.6 and fixed a bug in 'rsem-generate-data-matrix', which can cause 'rsem-find-DE' to crash
Bo Li [Mon, 15 Apr 2013 16:48:12 +0000 (11:48 -0500)]
Modifed README.md and WHAT_IS_NEW
Bo Li [Mon, 15 Apr 2013 16:26:02 +0000 (11:26 -0500)]
Modified wiggle.cpp & wiggle.h for more accurate floating point number arithmetics. Modified rsem-gen-transcript-plots to output warning messages instead of exit the script when positions where multiread track has less coverage than uniq track are detected. Thanks Han Lin for pointing out the problem and suggesting possible fixes
Bo Li [Mon, 15 Apr 2013 05:56:55 +0000 (00:56 -0500)]
Modified my_assert.h to postpone error message string generation
Bo Li [Fri, 5 Apr 2013 18:16:29 +0000 (13:16 -0500)]
Removed a too stringent sanity check in rsem-gen-transcript-plots
Bo Li [Wed, 27 Mar 2013 00:54:53 +0000 (19:54 -0500)]
remove .gitignore from the staging area
Bo Li [Fri, 22 Mar 2013 01:01:53 +0000 (20:01 -0500)]
Added some user-friendly error messages for BamConverter.h
Bo Li [Fri, 22 Mar 2013 00:43:06 +0000 (19:43 -0500)]
Modified rsem-tbam2gbam so that the original alignment quality MAPQ will be preserved if the input bam is not from RSEM
Bo Li [Sun, 27 Jan 2013 15:19:02 +0000 (09:19 -0600)]
Fixed a bug that will lead perl scripts fail to find the perl module they use
Bo Li [Thu, 24 Jan 2013 16:22:52 +0000 (10:22 -0600)]
Added user-friendly error messages if users forget to compile the source codes
Bo Li [Tue, 8 Jan 2013 16:11:50 +0000 (10:11 -0600)]
Fixed a bug in 'EBSeq/rsem-for-ebseq-generate-ngvector-from-clustering-info' which may crash the script
Bo Li [Mon, 7 Jan 2013 13:14:51 +0000 (07:14 -0600)]
Modified rsem-find-DE
Bo Li [Mon, 7 Jan 2013 13:11:20 +0000 (07:11 -0600)]
Updated EBSeq to v1.1.5
Bo Li [Fri, 30 Nov 2012 03:43:49 +0000 (21:43 -0600)]
- Added poly(A) tails to 'reference_name.transcripts.fa' so that the RSEM generated transcript unsorted BAM file can be fed into RSEM as an input file. However, users need to rebuild their references if they want to visualize the transcript level wiggle files and BAM files using IGV
- Modified 'rsem-tbam2gbam' to convert users' alignments from transcript BAM files into genome BAM files, provided users use 'reference_name.idx.fa' to build indices for their aligners
- Updated EBSeq from v1.1.3 to v1.1.4
- Corrected several typos in warning messages
Bo Li [Sun, 21 Oct 2012 19:41:38 +0000 (14:41 -0500)]
Updated EBSeq to v1.1.4
Bo Li [Thu, 18 Oct 2012 15:32:37 +0000 (10:32 -0500)]
Added --version option for rsem-calculate-expression
Bo Li [Wed, 10 Oct 2012 21:46:37 +0000 (16:46 -0500)]
use if/elsif to replace switch in rsem-calculate-expression
Bo Li [Mon, 24 Sep 2012 07:58:35 +0000 (02:58 -0500)]
Fixed a bug to make RSEM generated BAM file valid input for RSEM
Bo Li [Sat, 15 Sep 2012 20:27:44 +0000 (15:27 -0500)]
If a gene is not expressed, its length/effective length is defined as the unweighted mean of its isoforms'
Bo Li [Tue, 11 Sep 2012 10:10:36 +0000 (05:10 -0500)]
README.md is changed
Bo Li [Tue, 11 Sep 2012 09:07:43 +0000 (04:07 -0500)]
Added a script, 'rsem-find-DE', to run EBSeq automatically
Bo Li [Mon, 10 Sep 2012 21:22:52 +0000 (16:22 -0500)]
changed output format to contain FPKM etc. ; fixed a bug for paired-end reads
Bo Li [Fri, 27 Jul 2012 16:46:25 +0000 (11:46 -0500)]
Added a user-friendly error message for rsem-sam-validator
Bo Li [Mon, 23 Jul 2012 00:01:16 +0000 (19:01 -0500)]
Fixed a bug for calling pthread_join
Bo Li [Sun, 22 Jul 2012 02:11:07 +0000 (21:11 -0500)]
Fixed a bug in perl scripts for printing error messages
Bo Li [Sun, 15 Jul 2012 20:46:46 +0000 (15:46 -0500)]
Fix a bug on convert-sam-for-rsem for the case that a paired-end read can align to the same position with different directions
Bo Li [Mon, 2 Jul 2012 17:18:03 +0000 (12:18 -0500)]
rsem v1.1.21
Bo Li [Wed, 6 Jun 2012 02:02:46 +0000 (21:02 -0500)]
Tested the codes
Bo Li [Tue, 5 Jun 2012 21:25:13 +0000 (16:25 -0500)]
Made the BAM output of RSEM have all information contained in the input alignments file
Bo Li [Thu, 26 Apr 2012 13:50:22 +0000 (08:50 -0500)]
Included EBSeq for downstream differential expression analysis
Bo Li [Sun, 15 Apr 2012 13:27:02 +0000 (08:27 -0500)]
Added some instructions on how to visualize transcript coordinate BAM/WIG files using IGV
Bo Li [Sat, 14 Apr 2012 03:22:03 +0000 (22:22 -0500)]
Fixed a bug related to intermediate output displaying in wiggle.cpp
Bo Li [Fri, 13 Apr 2012 21:30:33 +0000 (16:30 -0500)]
Fixed a bug related to intermediate output displaying in EM.cpp
Bo Li [Wed, 21 Mar 2012 15:44:21 +0000 (10:44 -0500)]
Allowed > 2^31 hits
Bo Li [Sun, 11 Mar 2012 10:47:20 +0000 (05:47 -0500)]
Modified makefile to work for gcc version 4.5.3 or higher
Bo Li [Sun, 11 Mar 2012 10:22:22 +0000 (05:22 -0500)]
Modified 'convert-sam-for-rsem' so that this program will convert users' SAM/BAM files into acceptable BAM files for RSEM
Bo Li [Sun, 11 Mar 2012 04:35:10 +0000 (22:35 -0600)]
Add a validator for input SAM/BAM file
Bo Li [Fri, 9 Mar 2012 13:30:28 +0000 (07:30 -0600)]
Improved warning messages in rsem-gen-transcript-plots
Bo Li [Fri, 9 Mar 2012 04:36:05 +0000 (22:36 -0600)]
Add warning messages for detected invalid alignments
Colin Dewey [Mon, 27 Feb 2012 17:00:59 +0000 (11:00 -0600)]
Added .gitignore to ignore build products
Colin Dewey [Mon, 27 Feb 2012 16:56:16 +0000 (10:56 -0600)]
Modified build rules for sam/libbam.a to enable parallel build
Thanks to Tomoaki Nishiyama for the suggestion.
Bo Li [Sun, 19 Feb 2012 21:58:25 +0000 (15:58 -0600)]
[Change] Do not add --phred33-qual option if --no-qualities is enabled
Bo Li [Thu, 9 Feb 2012 00:07:26 +0000 (18:07 -0600)]
The order of @SQ tags in SAM/BAM files can be arbitrary now
Bo Li [Wed, 8 Feb 2012 16:38:25 +0000 (10:38 -0600)]
add --no-bam-output option to not generate output bam files
Bo Li [Wed, 8 Feb 2012 16:13:42 +0000 (10:13 -0600)]
roll back to original version plus fixed a small bug in calcCI.cpp
Bo Li [Wed, 8 Feb 2012 04:38:51 +0000 (22:38 -0600)]
rewrote parallelization of calcCI.cpp
Bo Li [Tue, 31 Jan 2012 16:24:31 +0000 (10:24 -0600)]
rsem v1.1.16
Bo Li [Thu, 26 Jan 2012 22:23:20 +0000 (16:23 -0600)]
rsem v1.1.15
Bo Li [Wed, 18 Jan 2012 05:36:57 +0000 (23:36 -0600)]
rsem v1.1.14
Bo Li [Sat, 31 Dec 2011 01:47:09 +0000 (19:47 -0600)]
relax the requirement about GTF attribute format
Bo Li [Wed, 14 Dec 2011 22:40:52 +0000 (16:40 -0600)]
modify one error message and add --bowtie-chunkmbs option by merging earonesty's change
Bo Li [Wed, 14 Dec 2011 22:07:06 +0000 (16:07 -0600)]
Merge remote-tracking branch 'origin/master'
Bo Li [Wed, 14 Dec 2011 22:04:59 +0000 (16:04 -0600)]
another change
bli25wisc [Wed, 14 Dec 2011 22:02:54 +0000 (14:02 -0800)]
Merge pull request #1 from earonesty/master
added --bowtie-chunkmbs
Erik Aronesty [Wed, 14 Dec 2011 18:29:20 +0000 (13:29 -0500)]
--bowtie-chunkmbs
Bo Li [Sat, 10 Dec 2011 23:44:50 +0000 (17:44 -0600)]
updated some description
Bo Li [Sat, 10 Dec 2011 00:00:47 +0000 (18:00 -0600)]
new update
Bo Li [Fri, 9 Dec 2011 23:57:17 +0000 (17:57 -0600)]
convert-sam-for-rsem is updated
Bo Li [Fri, 9 Dec 2011 23:53:11 +0000 (17:53 -0600)]
add a script to convert sam file for non-bowtie aligner
Bo Li [Sun, 4 Dec 2011 05:55:03 +0000 (23:55 -0600)]
rsem-v1.1.14b3
Bo Li [Fri, 2 Dec 2011 02:08:43 +0000 (20:08 -0600)]
rsem-1.1.14 with transcript wiggle plot generation
Bo Li [Thu, 1 Dec 2011 03:14:06 +0000 (21:14 -0600)]
add new files
Bo Li [Mon, 28 Nov 2011 23:21:26 +0000 (17:21 -0600)]
tested version for tbam2gbam