New in version 0.5.1 - September 2, 2013
Memory optimizations.
New in version 0.5 - August 28, 2013
Optimized the HapCompass algorithm. Users should see considerable speed-up in processing time.
New in version 0.4.1 - August 28, 2013
By default, HapCompass parses SAM/BAM files using a new algorithm that saves a temporary fragments file in the output directory.
New in version 0.4 - August 27, 2013
New and more efficient algorithm for loading in coordinate sorted SAM/BAM files.
More efficient algorithm for loading in name sorted SAM/BAM files.
Polyploid algorithm efficiency increased greatly.
New in version 0.3 - August 15, 2013
Processing multiple references in serial is now supported. It is still recommended to extract each reference and process in parallel. We are working on making the Picard parsing of the SAM/BAM files more efficient.
Added support for evaluating haplotype assemblies using the --evaluate and --phasing
Fixed a bug with processing long indels and complex variants.
New in version 0.2.3 - August 14, 2013
Fixed a bug introduced in 0.2.1 in printing the haplotype assembly to the solution file.
New in version 0.2.2 - August 14, 2013
Initial support for processing multiple VCF files.
Initial support for processing indels. For stable results, filter non-SNP variants from VCF file.
New in version 0.2.1 - August 13, 2013
Fixed bug with creating output file in a small number of cases.
Added debug option --debug
New in version 0.2 - August 12, 2013
Logging framework added.
Initial support for processing multiple reference sequences in serial.
Initial support for polyploid and cancer genomes (email Derek_Aguiar at brown dot edu for details).
New in version 0.7.1 - Feb. 24, 2014
HapCompass can now correctly handles variants with more than 2 alleles in the polyploid case. The diploid algorithm still expects at most 2 alleles per variant site.
New in version 0.7 - Feb. 23, 2014
HapCompass can now handle large ploidys, orders of magnitude faster than older versions.
New in version 0.6.3 - October 11, 2013
Fixed bug in edge case producing truncated assemblies.
Refactored.
New in version 0.6.3 - October 11, 2013
Fixed bug in edge case producing truncated assemblies.
Refactored.
New in version 0.6.1 - October 10, 2013
Removed unnecessary debug statements.
New in version 0.6 - October 3, 2013
New and more complete documentation.
Two new algorithms for processing polyploid and tumor genomes (see documentation).
An option added to prefer diverse edges in the compass graph for polyploid and tumor genomes (see documentation).
Code refactoring and now using Apache CLI to parse input parameters. WARNING: some parameter names have changed!
Faster processing when multiple references in the input.
New in version 0.5.4 - September 20, 2013
Minor updates in documentation; slightly more helpful debug information; removed excessive sysout printing.
New in version 0.5.3 - September 18, 2013
-r flag now correctly loads only the specified reference sequence from the VCF.
New in version 0.5.2 - September 17, 2013
Fixed bug where some variants were not being loaded from a polyploid VCF file.
This material is based upon work supported by the National Science Foundation under Grant Number 1048831 and 1321000. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
