Commit c2c6fee7 authored by Sander Bollen's avatar Sander Bollen
Browse files

dbsnp is not per se required

parent 86cbe6d0
...@@ -240,7 +240,7 @@ def create_primers_bwa(bam_handle, variant=None, region=None): ...@@ -240,7 +240,7 @@ def create_primers_bwa(bam_handle, variant=None, region=None):
def find_best_bwa(bam, variant=None, region=None, accept_snp=False, field=None, max_freq=None, dbsnp=None): def find_best_bwa(bam, variant=None, region=None, accept_snp=False, field=None, max_freq=None, dbsnp=None):
primers = [] primers = []
for primer in create_primers_bwa(bam, variant=variant, region=region): for primer in create_primers_bwa(bam, variant=variant, region=region):
if not accept_snp and max_freq is not None: if not accept_snp and max_freq is not None and dbsnp is not None:
prim = find_snps(primer, dbsnp, field) prim = find_snps(primer, dbsnp, field)
if prim.snp_freq <= max_freq: if prim.snp_freq <= max_freq:
primers.append(prim) primers.append(prim)
......
...@@ -163,7 +163,7 @@ def main(): ...@@ -163,7 +163,7 @@ def main():
"(qualities will be sanger-encoded 40)") "(qualities will be sanger-encoded 40)")
parser.add_argument('-R', '--reference', help="Path to reference fasta file", default=None, required=True) parser.add_argument('-R', '--reference', help="Path to reference fasta file", default=None, required=True)
parser.add_argument('--dbsnp', help="Path to DBSNP vcf", default=None, required=True) parser.add_argument('--dbsnp', help="Path to DBSNP vcf", default=None, required=False)
parser.add_argument('--primer3', help="Path to primer3_core exe", default=None, required=True) parser.add_argument('--primer3', help="Path to primer3_core exe", default=None, required=True)
parser.add_argument('--bwa', help="Path to BWA exe", default="bwa") parser.add_argument('--bwa', help="Path to BWA exe", default="bwa")
parser.add_argument('--samtools', help="Path to samtools exe", default="samtools") parser.add_argument('--samtools', help="Path to samtools exe", default="samtools")
......
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