ADD: data format for report in html. Use in FastQC step.
ADD: dependencies in pom.xml to Fastqc v0.11.2 to new step FastQC and a
related dependency to jbzip2.
ADD: add new step with Fastqc, it can be run on fastq or sam file and
generate an report html.
Merge branch 'master' into fastqcStep
ADD: FastQC can be run on fastq or sam file.
ADD: parameter on FastQC step for kmer-size, nogroup, expgroup, casava, nofilter option. Can be run with default value.
UPDATE: remove print test.
Merge branch 'master' into fastqcStep
UPDATE: In CheckerStep, now log data that is currently checked.
UPDATE: in execute method, exception message when throws an exception,
give to StepStatut instance.
UPDATE: remove used method to test and print message.
FIX: to manage 'input.format' option, replace convert in upper case to
lower case.
CHANGE: create new package for FastQC step. Compile class
mapping.AbstractFastQCStep and mapping.local.FastQCLocalStep in one
class in new package.
UPDATE: service file step.
UPDATE: remove convert list environment variables into array before
writing in file.
FIX: when check existence file, change limit on difference length
authorised. Now accept difference file length if it is inferior to 1% to
expected file length.
UPDATE: detail message return when an exception throws during execution
integration test.
Merge branch 'master' of https://code.google.com/p/eoulsan
Merge branch 'fastqcStep'