History¶
0.10.16 (05-10-2016)¶
- Modified
prepare-emase
so it can process the newest Ensembl gene annotation (Release 84) - The script
prepare-emase
can process gzipped files - Updated documentation
0.10.15 (05-04-2016)¶
- Uploaded to Anaconda.org
- Updated documentation
0.10.14 (04-25-2016)¶
- Added option to not having rname when loading/saving
AlignmentPropertyMatrix
- Documentation updated to reflect recent changes (e.g., processing paired-end data etc.)
0.10.12 (04-22-2016)¶
run-emase
report file names changed (effective -> expected)run-emase
report file can have notes
0.10.11 (02-15-2016)¶
- Minor change in documentation
0.10.9 (02-09-2016)¶
- Fixed readthedocs compiling fails
0.10.5 (01-20-2016)¶
- Added
pull_alignments_from
method inAlignmentPropertyMatrix
class - Added a script
pull-out-unique-reads
that unsets emase pseudo-alignments that are not uniquely aligning
0.10.3 (01-06-2016)¶
- Fixed a bug in
run-emase
on handling inbred (reference or one haplotype) alignments
0.10.2 (01-04-2016)¶
- Added
get-common-alignments
: To compute intersection between each of paired ends
0.9.10 (01-04-2016)¶
AlignmentMatrixFactory
can handle unmapped reads
0.9.8 (07-31-2015)¶
- Fixed a bug in
simulate-reads
: No more duplicate read ID’s
0.9.7 (07-28-2015)¶
- Added
create-hybrid
: Build hybrid target directly using custom transcripts - Added
simulate-reads
: Four nested models
0.9.6 (06-02-2015)¶
AlignmentPropertyMatrix
can represent an equivalence class- Fixed a bug in length normalization
- Swapped Model ID’s between 1 and 2
- Model 1: Gene->Allele->Isoform (*)
- Model 2: Gene->Isoform->Allele (*)
- Model 3: Gene->Isoform*Allele
- Model 4: Gene*Isoform*Allele (RSEM model)
0.9.5 (05-17-2015)¶
- Fixed length normalization: Depth = Count / (Transcript_Length - Read_Length + 1)
0.9.4 (02-23-2015)¶
- Fixed a bug in
prepare-emase
0.9.3 (02-22-2015)¶
- Fixed a bug in Model 2 of handling multireads
run-emase
checks absolute sum of error (in TPM) for termination
0.9.2 (02-17-2015)¶
- Added three more models of handling multireads
- Model 1: Gene->Isoform->Allele
- Model 2: Gene->Allele->Isoform
- Model 3: Gene->Isoform*Allele
- Model 4: Gene*Isoform*Allele (RSEM model)
0.9.0 (01-31-2015)¶
- First release on PyPI
- Only implements RSEM model for handling Multiply-mapping reads (or multireads)