ADD: features to improve the output Overrepresented Sequences module
from FastQC : for sequences 'no hit' (not found in contaminants list), a
blastn is launched, the best hit with 100% identity and 0% gaps replace
'no hit'. Optional, configuration in aozan.conf.
UPDATE: modify byte code of FastQC for class ContaminantFinder,
according to blast needed for FastQC in aozan.conf.
ADD: if step Blast is needed, configure this step and patch the byte
code from FastQC for call the method implemented in Aozan.
ADD: parameters for step blast, call in OverrepresentedSequences modules
from FastQC.
FIX: replace Map by ConcurrentMap for save result blastn search and
remove printStackTrace() in blocs try-catch .
UPDATE: javadoc
ADD: class utility method to extract information from xml file.
ADD: logo Aozan transparent for qc report.
FIX: parameter included in configuration, check is null or empty.
UPDATE: error message while error computing occurs.
UPDATE: throws exception, message added in logger.
UPDATE: xsl files for qc report FastQC and FastQ Screen.
ADD: formatter date used in qc report Fastqc and FastQScreen xml files.
ADD: mapper and arguments uses by fastqscreen is now parameters in
configuration aozan. Possibility to call all mapper define in Eoulsan
(Bowtie2, BWA, GSNAP). Default value is bowtie, with arguments define in
FastQScreen code.
UPDATE: class demo and wrapped AozanException for debugging code.
FIX: catch exception.
FIX: update map with sequence and BlastResultHit before launching Blast
to remove to call blast several time for the same sequence.
UPDATE: aozan.xsl, change css.
ADD: in module blast for overrepresented sequences, add the possibility
to use a list of sequences to do not analysis with blastn.
UPDATE: warning message when not enough space in storage disk.