#/*******************************************************************************
# * Contributors:
# *    Susanna Zucca, Margherita Villaraggia - susanna.zucca(at)unipv.it
# *******************************************************************************/

###############################################################################
#print_primer_seq.pl
###############################################################################
#==============================================================================
#title           :print_primer_seq.pl
#description     :This script taks as input Illumina Manifest File and provides as output two txt files containing the list of ULSO and DLSO primers.
#authors         :Susanna Zucca, Margherita Villaraggia
#date            :20160216
#version         :1.0   
#usage		 :perl print_primer_seq.pl /Path/to/Manifest.txt
#example      	 :perl print_primer_seq.pl Example_manifest.txt
#==============================================================================


###############################################################################
#trimming.pl
###############################################################################
#==============================================================================
#title           :trimming.pl
#description     :This script taks as input paired-end FastQ files and R1 and R2 primer lists (generated by print_primer_seq.pl) and provides as output R1.trim.fastq and R2.trim.fastq fastq files with trimmed reads. Primer_id.txt file is generated, required to remove reads with reads_remove.pl script
#authors         :Susanna Zucca, Margherita Villaraggia
#dependencies    :List::Util
#date            :20160216
#version         :1.0   
#usage		 :perl trimming.pl Sample_R1.fastq Sample_R2.fastq R1_primer.txt R2_primer.txt
#notes		 :R1_primer.txt and R2_primer.txt are generated by print_primer_seq.pl
#example	 :perl trimming.pl Example_R1.fastq Example_R2.fastq Example_manifest.txt_Primer_R1.txt Example_manifest.txt_Primer_R2.txt
#==============================================================================


###############################################################################
#reads_remove.pl
###############################################################################
#==============================================================================
#title           :reads_remove.pl
#description     :This script taks as input trimmed paired-end FastQ files, vcf file (generated by any variant caller after alignment) and provides as output R1.reads_remove.fastq and R2.reads_remove.fastq fastq files with removed all reads generated by a primer pairing with a region containing a mutation reported in vcf file.
#authors         :Susanna Zucca, Margherita Villaraggia
#dependencies    :List::Util
#date            :20160216
#version         :1.0   
#usage		 :perl trimming.pl Sample_R1.fastq Sample_R2.fastq R1_primer.txt R2_primer.txt
#notes		 :R1_primer.txt and R2_primer.txt are generated by print_primer_seq.pl
#example	 :perl reads_remove.pl Example_R1.fastq.trim.fastq Example_R2.fastq.trim.fastq Example.vcf Example_R1.fastq_primer_ID.txt Example_manifest.txt_Primer_R2.txt
#==============================================================================

##############################################################################
#Example of trimming pipeline:
##############################################################################

perl print_primer_seq.pl Example_manifest.txt
perl trimming.pl Example_R1.fastq Example_R2.fastq Example_manifest.txt_Primer_R1.txt Example_manifest.txt_Primer_R2.txt
[Alignment and variant calling]
perl reads_remove.pl Example_R1.fastq.trim.fastq Example_R2.fastq.trim.fastq Example.vcf Example_R1.fastq_primer_ID.txt Example_manifest.txt_Primer_R2.txt