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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 in AlignmentPropertyMatrix 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)