From 480ae2c5a81be2b40815b35086cf38733e4bdf24 Mon Sep 17 00:00:00 2001 From: Matt MacManes Date: Fri, 4 Dec 2015 14:42:01 -0500 Subject: [PATCH 1/2] we're always passing a fastq this solves (I think) https://github.com/Blahah/transrate/issues/157 --- lib/transrate/snap.rb | 1 + 1 file changed, 1 insertion(+) diff --git a/lib/transrate/snap.rb b/lib/transrate/snap.rb index fbbe937..14f63e9 100644 --- a/lib/transrate/snap.rb +++ b/lib/transrate/snap.rb @@ -37,6 +37,7 @@ def build_paired_cmd l, r, threads cmd << " -D 5" # extra edit distance to search. needed for -om cmd << " -om 5" # Output multiple alignments. extra edit distance cmd << " -omax 10" # max alignments per pair/read + cmd << " -fastq" # we're always passing a fastq cmd end From dd28f268d8494e1930673bf9d3b4be7bbbd7e34a Mon Sep 17 00:00:00 2001 From: Matt MacManes Date: Fri, 4 Dec 2015 17:08:35 -0500 Subject: [PATCH 2/2] update to -pairedFastq ready for merge? --- lib/transrate/snap.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/transrate/snap.rb b/lib/transrate/snap.rb index 14f63e9..8c480f3 100644 --- a/lib/transrate/snap.rb +++ b/lib/transrate/snap.rb @@ -37,7 +37,7 @@ def build_paired_cmd l, r, threads cmd << " -D 5" # extra edit distance to search. needed for -om cmd << " -om 5" # Output multiple alignments. extra edit distance cmd << " -omax 10" # max alignments per pair/read - cmd << " -fastq" # we're always passing a fastq + cmd << " -pairedFastq" # we're always passing a fastq cmd end