def add(self, contigfile, sampleid, species, bamfile=None, assembler=None, copy=False) :
self.log.info("adding %s (%s, %s, %s, %s)" % (sampleid, species, contigfile, bamfile, assembler))
if self.contains(sampleid) :
self.log.warn("%s is already present, overwriting..." % sampleid)
contigfile = self.copy(contigfile) if copy else abspath(contigfile)
bamfile = self.copy(bamfile) if copy else abspath(bamfile) if bamfile else bamfile
self.params['samples'][sampleid] = { 'contigs' : contigfile,
'contigs_checksum' : md5(contigfile),
'species' : species,
'bam' : bamfile,
'bam_checksum' : md5(bamfile) if bamfile else None,
'assembler' : assembler }
self.set_sample_checksum()
def checksum(self) :
return md5(self.fname)
