Mercurial > repos > clifinder > clifinder
changeset 16:40695c10cfbd draft
"planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 248ea88d1c69b80fb3a380e674f83de236129601"
| author | clifinder |
|---|---|
| date | Thu, 13 Feb 2020 08:37:34 -0500 |
| parents | 6d7caeea1e74 |
| children | 3e3370387441 |
| files | script/CLIFinder.pl |
| diffstat | 1 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- a/script/CLIFinder.pl Wed Feb 12 05:32:38 2020 -0500 +++ b/script/CLIFinder.pl Thu Feb 13 08:37:34 2020 -0500 @@ -97,7 +97,7 @@ print STDOUT "Alignment of $name[$tabR] to L1\n"; my $sam = $html_repertory.'/'.$name[$tabR]."_L1.sam"; push(@garbage, $sam); - align_paired( $TE, $fastq1[$tabR], $fastq2[$tabR], $sam, $threads, $mis_auth); + halfmap_paired($TE, $fastq1[$tabR], $fastq2[$tabR], $sam, $threads, $mis_auth); print STDOUT "Alignment done\n"; ################################################## @@ -656,7 +656,7 @@ } ############################################################ -##Function that aligned paired-end reads on a referential### +##Function to get half-mapped paired-end reads on a ref # ############################################################ ## @param: # ## $index: referential file # @@ -666,7 +666,7 @@ ## $threads: number of threads used # ## $mis: tolerated mismatches # ############################################################ -sub align_paired +sub halfmap_paired { my ($index, $fastq1, $fastq2, $sam, $threads, $mis) = @_ ; my @garbage = (); @@ -677,7 +677,7 @@ `bwa aln -n $mis -t $threads $index $fastq1 > $sai1`; `bwa aln -n $mis -t $threads $index $fastq2 > $sai2`; - `bwa sampe $index $sai1 $sai2 $fastq1 $fastq2 > $sam`; + `bwa sampe $index $sai1 $sai2 $fastq1 $fastq2 | samtools view -@ $threads -h -F 2 -G 12 -o $sam`; ## delete temporary single aligned files unlink @garbage;