def sort_by_pos(input_file,output_file):
n = num_thread2use(trim_batch,len(fastqFiles),thread)
sortBam(input_file,output_file,n,sortType='pos')
disc = input_file[:-3] + 'disc.sam'
disc_sort = output_file[:-3] + 'disc.bam'
sortBam(disc,disc_sort,n,sortType='pos')
split = input_file[:-3] + 'split.sam'
split_sort = output_file[:-3] + 'split.bam'
sortBam(split,split_sort,n,sortType='pos')
def sort_by_pos(input_file, output_file):
n = num_thread2use(trim_batch, len(fastqFiles), thread)
sortBam(input_file, output_file, n, sortType='pos')
disc = input_file[:-3] + 'disc.sam'
disc_sort = output_file[:-3] + 'disc.bam'
sortBam(disc, disc_sort, n, sortType='pos')
split = input_file[:-3] + 'split.sam'
split_sort = output_file[:-3] + 'split.bam'
sortBam(split, split_sort, n, sortType='pos')
def sort_by_name(input_file, output_file):
n = num_thread2use(trim_batch, len(fastqFiles), thread)
sortBam(input_file, output_file, n, sortType='name')
stat = sarge.get_stdout('samtools flagstat {bam}'.format(bam=output_file))
with open(output_file[:-3] + 'flagstat.txt', 'w') as f:
f.write(stat)
def sort_by_pos(input_file, output_file):
n = num_thread2use(trim_batch, len(fastqFiles), thread)
sortBam(input_file, output_file, n, sortType='pos')
def sort_by_name(input_file,output_file):
n = num_thread2use(trim_batch,len(fastqFiles),thread)
sortBam(input_file,output_file,n,sortType='name')
stat = sarge.get_stdout('samtools flagstat {bam}'.format(bam=output_file))
with open(output_file[:-3]+'flagstat.txt','w') as f:
f.write(stat)
def sort_by_pos(input_file,output_file):
n = num_thread2use(trim_batch,len(fastqFiles),thread)
sortBam(input_file,output_file,n,sortType='pos')
def run_sortBam(input_file, output_file):
sortBam(input_file, output_file, thread)
def run_sortBam(input_file,output_file):
sortBam(input_file,output_file,thread)
