From cf52e37b66f7a2229990c23f7d9a7f818dc334aa Mon Sep 17 00:00:00 2001 From: Simon Ye Date: Wed, 10 Feb 2016 15:11:03 -0500 Subject: [PATCH] Remove interleaved fastq tip in bamToFastq Redirecting to the interleaved file is a buffered process leading to garbled output on some platforms. It's probably best to just join the paired fastqs with another command. --- src/bamToFastq/bamToFastqMain.cpp | 5 ----- 1 file changed, 5 deletions(-) diff --git a/src/bamToFastq/bamToFastqMain.cpp b/src/bamToFastq/bamToFastqMain.cpp index f2102ae98..9cbb269e9 100644 --- a/src/bamToFastq/bamToFastqMain.cpp +++ b/src/bamToFastq/bamToFastqMain.cpp @@ -132,11 +132,6 @@ void bamtofastq_help(void) { cerr << "\t-tags\tCreate FASTQ based on the mate info" << endl; cerr << "\t\tin the BAM R2 and Q2 tags." << endl << endl; - - cerr << "Tips: " << endl; - cerr << "\tIf you want to create a single, interleaved FASTQ file " << endl; - cerr << "\tfor paired-end data, you can just write both to /dev/stdout:" << endl << endl; - cerr << "\tbedtools bamtofastq -i x.bam -fq /dev/stdout -fq2 /dev/stdout > x.ilv.fq" << endl << endl; exit(1); }