#! /bin/bash

cd $(dirname $0)


for echantillon in 003GIDAB6_S22_R1_001.fastq.gz 005GIDAB9_S23_R1_001.fastq.gz 019GIDLBAPAVM_S24_R1_001.fastq.gz 025ESTAB3_S13_R1_001.fastq.gz 026ESTAB6_S14_R1_001.fastq.gz 027ESTLBA9_S15_R1_001.fastq.gz 028MAIAB3_S16_R1_001.fastq.gz 029MAIAB9_S17_R1_001.fastq.gz 030MAIAB15_S18_R1_001.fastq.gz 031LAMAB3_S6_R1_001.fastq.gz 032LAMAB9_S7_R1_001.fastq.gz 033GHOAB3_S8_R1_001.fastq.gz 034GHOAB9_S9_R1_001.fastq.gz 036BOIAB3_S1_R1_001.fastq.gz 037BOIAB9_S2_R1_001.fastq.gz 038BOILBA11_S3_R1_001.fastq.gz 039COUAB3_S4_R1_001.fastq.gz 040COUAB9_S5_R1_001.fastq.gz 041LASAB3_S10_R1_001.fastq.gz 042LASAB9_S11_R1_001.fastq.gz 043HOFAB4_S19_R1_001.fastq.gz 046HOFAB9_S20_R1_001.fastq.gz 047HOFAB12_S21_R1_001.fastq.gz 048T3_S12_R1_001.fastq.gz


do
 

echo java -da -Xmx400m -cp C:\/Users\/Julien\/Desktop\/bbmap\/current jgi.BBMerge in1=C:\/Users\/Julien\/Desktop\/reads\/P18006_smd_nextseq\/fastq\/"$echantillon" in2=C:\/Users\/Julien\/Desktop\/reads\/P18006_smd_nextseq\/fastq\/$(echo $echantillon |sed 's/R1/R2/') out=C:\/Users\/Julien\/Desktop\/bbmerge\/merged\/out\/$(echo $echantillon |cut -c1-10)_dna_merged.fastq outu=C:\/Users\/Julien\/Desktop\/bbmerge\/merged\/outu\/$(echo $echantillon |cut -c1-10)_dna_unmerged.fastq

echo 

done
 
