UPDATE: Add mapper and genome words to eoulsan.dic.
UPDATE: In Version, add lessThan(), lessThanOrEqualTo(), greaterThan() and greaterThanOrEqualTo() methods.
FIX: For Bowtie 1, the new binaries names are used since 1.1 not 1.0.
FIX: Bowtie 2 now works with Bowtie 2 version greater of equal to 2.2.
UPDATE: The readsmapper system can now handle mapper flavor (e.g. large-index). Not that feature is not currently handle by Eoulsan steps.
UPDATE: In AbstractFilterAndMapReadsStep, use a switch/case to handle mapper parameters.
UPDATE: IN AbstractReadsMapperStep and AbstractFilterAndMapReadsStep, use common constants for mapper parameters names.
UPDATE: Remove old compatibility "mapperarguments" parameter name for mapper steps.
FIX: For Bowtie 1 and 2, fix the extension of the index for large-index flavor.
FIX: For Bowtie 1, the name of the binary is bowtie-align since 1.1.
UPDATE: mapreads and filterandmap steps now handle mapper version and flavor.
UPDATE: GenomeMapperIndexGeneratorStep now handle version and flovor of mappers.
UPDATE: In SimpleGenomeIndexStorage, the checksum used to identify mapper index, now use mapper name, version and flavor, in addition of genome checksum.
UPDATE: In SequenceReadsMapper, add getIndexerArguments(), getListIndexerArguments() and setIndexerArguments() methods.
UPDATE: Update STARReadsMapper.getIndexerCommand() to use getListIndexerArguments().
ADD: Add a new step called "starindexgenerator" that allow to create a custom STAR mapper index.
UPDATE: Update GenomeIndexStorage to use the additionnal parameter of the "starindexgenerator" step in the checksum to identify the right index.
FIX: In STARIndexGenerator, forget to handle some parameter in configure().
DOC: Update documentation for mappers and the new createstarmapperindex step.