Release v2018.06.28

• Add option to specify the maximum number of missed cleavages (thanks to Sean at CWRU-CPB)
• Make command line argument names case-insensitive
• Add additional checks to prevent the output of duplicate peptide evidences (fixes Issue #24)

Release v2018.04.09

• When the EnzymeID is 9 (NoCleavage) do not cleavage after any residue
  • Previously EnzymeID 0 and EnzymeID 9 were identical. Now EnzymeID 0 cleaves after every residue while EnzymeID 9 won't cleave after any residue (useful for peptidomics)
• Update help documentation
• Allow the FASTA file to have extension .faa (in addition to .fasta or .fa)
• When examining existing index files, allow for a 2 second variance between the LastModified time stored in the file and the time reported by the operating system for the file

Release v2018.01.30

• MzIdentML creation: Don't output an empty ModificationParams element when there are no modifications (because not including it complies with the XML Schema, while including it with no child nodes does not)
• Java 9 compatibility: add dependencies on com.sun.xml.bind:jaxb-impl and jaxb:activation to support use with Java 9 (with some warnings). Without this change, users must supply the Java VM argument "--add-modules=java.xml.bind,java.activation"

Release v2017.08.23+

• Fix a problem with peptide ID creation that was leading with reference issues in the mzid files.
• Fix a usage typo #15

Release 2017.07.21

• Performance improvements when reading mzML and mzIdentML files
• Add scoring parameters for UVPD TMT6Plex
• Improve the error message displayed when there are too many duplicate proteins
• ScoringParamGen:
  • Write and keep the converted TSV files to reduce time to re-run training on the same data
  • Write both the binary and text versions of the training results
  • Run multithreaded

Release 2017.01.27

• Reduce the number of exceptions seen when a thread exits with an exception - There were multiple exceptions being displayed that were the result of killing the other threads.
• Change how the overall progress reporting and exception handling is managed, to minimize the thread overhead burden.
• Allow the user to specify a number of tasks on the command line using "-tasks n", and modify the default calculation. The previous default had a hard-coded limit of 64, and multiplied the number of threads by 10; new default removes the hard-coded limit, and multiplies by only 3.
• Change the output behavior - by default, the per-thread status messages will no longer be output. Per-thread status messages are a large amount of output, and aren't usually necessary with good progress reporting. The old output can be re-enabled using the command line argument "-verbose 1"
• Add the elapsed time to the overall progress report
• Fix the overall progress reporting - get the active task progress again with the overall task progress.

Release 2017.01.10

First binary release on GitHub