Release for DOI

Release with all commits since VS1.0.6 for generating a DOI.

Fourth release of CCseqBasic Stable (CCseqBasicS)

Changed default colors from red-green to color blindness friendly magenta-turquoise. Old colors can be requested with flag --redGreen .

Brought in multilane fastq support, by introducing parameter file PIPE_fastqPaths.txt , and gzipped fastq file support with flag --gz .

Introduced flag --onlyBlat to allow generating homology-region filter separately, before running the production runs.

Brought in integral Tri-C analysis, to support libraries directed to 3-way (instead of 2-way) interaction analysis : integrated Marieke Oudelaar's Tri-C codes into the CCseqBasicS release. These can be directed with flags --triC --triCwithExcl --onlyTriC --triCbin --triCmax

Third release of CCseqBasic Stable (CCseqBasicS) , generated 9th March 2018.

This release is stable.

This release includes all first-round portability testing bug fixes and tool version support fixes,
based on feedback of external testers.

Also added flag --useSymbolicLinks which gives support to small public server spaces : if this flag is set, the bigwigs will be symlinked to the public area, instead of actually storing them there.

Second release of CCseqBasic Stable (CCseqBasicS)

Second release of CCseqBasic Stable (CCseqBasicS) , generated 5th March 2018.

The release was generated to mark the second stable portable development stage.

This release includes some new features from the development pipe CCseqBasic5 ( including bowtie2 support and '--onlyCis' run mode).
So if you are are interested in using the new features with a stable pipeline, this is probably your choice.

This version has been tested both intra-house and externally, and it is stable.

This release is essentially the development pipe version 1.0.0 ( https://github.com/Hughes-Genome-Group/CCseqBasic5/releases/tag/v1.0.0 ) , complemented with the bug fixes of commits 1d36bcb and 0f188bf , and new flash versions support fix 6dce817

First release of CCseqBasic Stable (CCseqBasicS)

First release of CCseqBasic Stable (CCseqBasicS) , generated 5th March 2018.

The release was generated to mark the first stable portable development stage.

This version has been tested both intra-house and externally, and it is stable.

This release should be more stable than the one following it, so if you are are only interested in
running the pipe, and not using the new features, this is probably your choice.