Add the SA-IS algorithm
Add Doxygen to the project to build documentation
Add python 2, python3, perl, lua, java build targets if possible.
Add skiplists template, then convert sparse-bitpacked-array to C++ and use the sparse lists
Add highly optimized perfect alignment algorithm
Add a 2D matrix which uses skiplists in rows and columns
Re-evaluate Upper-diagonal-square-matrix functions to make index correlation more regular, make getSize() a const_expr if applicable.
Incorporate useful parts of PEPIS http://bioinfo.noble.org/PolyGenic_QTL/Download.gy
Add GEO .soft file tests
Add GEO .soft file helper functions to extract information related to GDS, GSM, GPL subtypes.
Add benchmarking portions in test/
Evaluate and incorporate the following repsoitories: http://www.biostat.jhsph.edu/~hji/cisgenome/index_files/manual.htm https://www.sanger.ac.uk/science/tools/caf https://github.com/ComparativeGenomicsToolkit/cactus https://github.com/fukunagatsu/CapR https://code.google.com/archive/p/cbrowse/ https://code.google.com/archive/p/campways/ https://sourceforge.net/projects/chipmeta/files/?source=navbar https://github.com/voges/calq http://www.ccp4.ac.uk/ https://github.com/KarchinLab/CHASMplus http://ruby.chemie.uni-freiburg.de/~martin/chemtool/ http://emboss.open-bio.org/rel/rel6/apps/cacheensembl.html http://emboss.open-bio.org/rel/rel6/apps/cachedas.html https://sourceforge.net/projects/wgs-assembler/files/?source=navbar http://www.htslib.org/ http://clark.cs.ucr.edu/ https://github.com/trinityrnaseq/trinityrnaseq/wiki https://github.com/mcveanlab/mccortex http://abacus.gene.ucl.ac.uk/software/paml.html https://sourceforge.net/projects/chipotle-2/files/chipotle-2/ChIPOTle2.0/ http://mrfast.sourceforge.net/ http://bioinf.gen.tcd.ie/~faresm/software/software.html#caps2 http://bioinfo.cnio.es/index.php/services/bioinfotools/22-cargo-cancer-and-related-genes-online http://boevalab.com/FREEC/ https://sourceforge.net/projects/coperead/ https://github.com/kaibader/CaSSiS https://www.openms.de/ https://github.com/tingchenlab/CROP https://simtk.org/projects/campaign https://sourceforge.net/projects/camino-trackvis/files/0.2/ https://sourceforge.net/projects/camino-trackvis/files/ERN/ https://sourceforge.net/projects/kakscalculator2/ http://www.xavierdidelot.xtreemhost.com/clonalframe.htm?i=2 https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download https://github.com/abhatta3/Condition-dependent-Correlation-Subgroups-CCS https://bitbucket.org/Wenan/caviarbf/src/7e428645be5eb518eebf8df18b436c3eca898ca2/src/?at=default https://github.com/cambDI/camb https://sites.google.com/site/pierrickcoupe/softwares/denoising-for-medical-imaging/multiphoton-filtering http://www.bioinformatics.org/cgi-bin/viewvc.cgi/catch/ http://emboss.open-bio.org/html/use/apbs04.html#EMBOSSAppsTableR6 http://emboss.open-bio.org/html/use/apbs05.html http://emboss.open-bio.org/html/dev/ch01s02.html https://github.com/Illumina/canvas https://www.bsse.ethz.ch/cbg/software/ct-cbn.html https://github.com/grenaud/bedBamAndBeyond/ https://sourceforge.net/projects/seqgenomebrowse/ http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/filter-it/1.0.2/filter-it.html http://noch.sourceforge.net/ https://github.com/hyunminkang/apigenome https://github.com/GreenleafLab/motifmatchr/ https://github.com/labsquare/fastQt https://github.com/cschlaffner/PoGo https://biosails.github.io/pheniqs/ https://github.com/smith-chem-wisc/mzLib https://sourceforge.net/projects/ncl/ https://github.com/kdmurray91/libqes https://bitbucket.org/mzytnicki/multi-mapping-counter https://sourceforge.net/projects/libgdf/ https://sourceforge.net/projects/htqc/ https://sourceforge.net/projects/lwgv/files/?source=navbar https://sourceforge.net/projects/skittle/ https://sourceforge.net/projects/quicktsaf/files/?source=navbar http://www.g-language.org/kbws/ http://bioinfo.single-cell.cn/rna-qc-chain.html https://github.com/mirand863/gcsplit http://www.bcgsc.ca/platform/bioinfo/software/laneruler http://www.metatrans.org/ https://bitbucket.org/ball/ball https://github.com/davidhwyllie/findNeighbour http://sparx-em.org/sparxwiki/ https://github.com/vincent-picaud/Joint_Baseline_PeakDeconv https://code.google.com/archive/p/ftdr/ http://gedas.bizhat.com/gedas.htm https://github.com/imgag/ngs-bits https://sourceforge.net/projects/samstat/ https://sourceforge.net/projects/gen3d/ http://mycor.nancy.inra.fr/egglib/ https://www2.mrc-lmb.cam.ac.uk/relion/index.php?title=Main_Page https://github.com/lorinanthony/MAPIT https://github.com/tsirigos/ibm-cbc-genomic-tools https://github.com/wingolab-org/pecaller http://www.bioinf.org.uk/software/bioplib/ https://github.com/3DGenomes/binless https://github.com/walaj/VariantBam https://github.com/LohmuellerLab/PReFerSim https://github.com/FePhyFoFum/phyx https://code.google.com/archive/p/libzerg/ http://users-cs.au.dk/cstorm/software/tqdist/ https://github.com/ABI-Software/ICMA https://github.com/slowkow/snpsea/ https://github.com/MWSchmid/Rcount https://github.com/danmaclean/2kplus2 https://cran.r-project.org/web/packages/graphkernels/index.html https://sourceforge.net/projects/whiteboard-class/ https://github.com/terraphast/terraphast https://github.com/jujubix/rnadecoder https://sourceforge.net/projects/starrynite/ https://openstructure.org/docs/1.7.1/install/ https://github.com/MWSchmid/HiCdat https://github.com/yarden/MISO https://github.com/genome/breakdancer https://github.com/szpiech/garlic https://github.com/TimeDependentChipSeqAnalyser/TDCA https://chaste.cs.ox.ac.uk/trac/wiki/ChasteGuides/AccessCodeRepository https://sourceforge.net/projects/pysces/ https://bitbucket.org/tobiasmarschall/clever-toolkit https://sourceforge.net/projects/cdaotools/ https://github.com/cosmo-team/cosmo/tree/VARI-merge https://github.com/arq5x/bedtools2 https://sourceforge.net/projects/chip-seq/files/chip-seq/1.5.3/ https://github.com/osallou/cassiopee-c https://github.com/gersteinlab/MUSIC https://liberles.cst.temple.edu/Software/CASS/index.html#Download https://sourceforge.net/p/ccpn/code/HEAD/tree/branches/stable/ccpn/ https://github.com/nedaz/cola https://hive.biochemistry.gwu.edu/dna.cgi?cmd=censuscope https://sourceforge.net/projects/xat/files/CAT/0.8.6/ http://emboss.open-bio.org/html/use/apbs06.html https://code.google.com/archive/p/mesquitegsoc09/source/default/source https://github.com/pjotrp/biopp/tree/master https://github.com/samtools/samtools