From 76bb04f3b7559b1344b223f7b46ec5147cdd3568 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Tue, 24 Aug 2010 21:32:06 +0000 Subject: [PATCH] Better detect which program ids generated CNF4 srf files. apparently illumina2srf v1.11.5Illumina.1.3 also genrated CNF4s. It's only illumina2srf v1.11.6... that generated CNF1s. --- scripts/srf2named_fastq.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/scripts/srf2named_fastq.py b/scripts/srf2named_fastq.py index 7bfc4da..d0403f6 100755 --- a/scripts/srf2named_fastq.py +++ b/scripts/srf2named_fastq.py @@ -63,10 +63,10 @@ You can also force the flowcell ID to be added to the header.""") help="add flowcell id header to sequence") parser.add_option('-l','--left', default="r1.fastq", help='left side filename') - parser.add_option('-r','--right', default="r2.fastq", - help='right side filename') parser.add_option('-m','--mid', default=None, help='actual sequence mid point') + parser.add_option('-r','--right', default="r2.fastq", + help='right side filename') parser.add_option('-s','--single', default=None, help="single fastq target name") parser.add_option('-v', '--verbose', default=False, action="store_true", @@ -190,6 +190,8 @@ def is_cnf1(filename): """ max_header = 1024 ** 2 PROGRAM_ID = 'PROGRAM_ID\000' + cnf4_apps = set(("solexa2srf v1.4", + "illumina2srf v1.11.5.Illumina.1.3")) if not is_srf(filename): raise ValueError("%s must be a srf file" % (filename,)) @@ -204,7 +206,7 @@ def is_cnf1(filename): f.close() os.close(fd) - if program_id_header == "solexa2srf v1.4": + if program_id_header in cnf4_apps: return False else: return True -- 2.30.2