#!/bin/bash
module load bioinfo/samtools-1.16.1

# genome (fasta)
#samtools faidx /work/project/bbdata/workdir/zymoseptoria_egip/gene_prediction/LoReAN/ztritici_data/Mygr_323_reformat_with_mito.clean.fsa "chr_8" > ztIPO323.chr8.fasta
#samtools faidx /work/project/bbdata/workdir/zymoseptoria_egip/PERSIST/assembly/CF2008.assembly.fasta "chr_8" > g1.chr8.fasta
#samtools faidx /work/project/bbdata/workdir/zymoseptoria_egip/PERSIST/assembly/SE128.assembly.fasta "chr_8" > g2.chr8.fasta
#samtools faidx raw/ncbi-genomes-2022-11-30/GCA_900091695.1_Zt_ST99CH_3D7_genomic.fna "LT853699.1" | sed 's/LT853699.1/ST99CH_3D7_chr8/' > ST99CH_3D7.chr8.fasta
#samtools faidx raw/ncbi-genomes-2022-11-30/GCA_900099495.1_ZT1A5_complete_assembly_genomic.fna "LT882683.1" | sed 's/LT882683.1/ST99CH_1A5_chr8/' > ST99CH_1A5.chr8.fasta
#samtools faidx raw/ncbi-genomes-2022-11-30/GCA_900184105.1_ST99CH_3D1_genomic.fna "LT854280.1" | sed 's/LT854280.1/ZT3D1_chr8/' > ZT3D1.chr8.fasta
#samtools faidx raw/ncbi-genomes-2022-11-30/GCA_900184115.1_ST99CH_1E4_genomic.fna "LT854260.1" | sed 's/LT854260.1/ZT1E4_chr8/' > ZT1E4.chr8.fasta

# pop (fastq)
#path=/work/project/baric/BIOGER/APOGE_2022
#genome=INRA18-TM0001
#pop=pop1
#gen=g1
#samtools index ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam
#samtools view -hb ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam "gnl|Mygr_323|chr_8" > ${pop}_${gen}.bam
#samtools fastq ${pop}_${gen}.bam -1 ${pop}_${gen}.R1.fastq.gz -2 ${pop}_${gen}.R2.fastq.gz -s ${pop}_${gen}.single.fastq.gz
#
#genome=INRA18-TM0011
#gen=g2
#samtools index ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam
#samtools view -hb ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam "gnl|Mygr_323|chr_8" > ${pop}_${gen}.bam
#samtools fastq ${pop}_${gen}.bam -1 ${pop}_${gen}.R1.fastq.gz -2 ${pop}_${gen}.R2.fastq.gz -s ${pop}_${gen}.single.fastq.gz
#
#genome=INRA18-TM0018
#gen=g3
#samtools index ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam
#samtools view -hb ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam "gnl|Mygr_323|chr_8" > ${pop}_${gen}.bam
#samtools fastq ${pop}_${gen}.bam -1 ${pop}_${gen}.R1.fastq.gz -2 ${pop}_${gen}.R2.fastq.gz -s ${pop}_${gen}.single.fastq.gz
#
#genome=INRA18-TM0066
#gen=g4
#samtools index ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam
#samtools view -hb ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam "gnl|Mygr_323|chr_8" > ${pop}_${gen}.bam
#samtools fastq ${pop}_${gen}.bam -1 ${pop}_${gen}.R1.fastq.gz -2 ${pop}_${gen}.R2.fastq.gz -s ${pop}_${gen}.single.fastq.gz
#
#genome=INRA18-TM0080
#gen=g5
#samtools index ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam
#samtools view -hb ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam "gnl|Mygr_323|chr_8" > ${pop}_${gen}.bam
#samtools fastq ${pop}_${gen}.bam -1 ${pop}_${gen}.R1.fastq.gz -2 ${pop}_${gen}.R2.fastq.gz -s ${pop}_${gen}.single.fastq.gz
#
#genome=INRA18-TM0112
#gen=g6
#samtools index ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam
#samtools view -hb ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam "gnl|Mygr_323|chr_8" > ${pop}_${gen}.bam
#samtools fastq ${pop}_${gen}.bam -1 ${pop}_${gen}.R1.fastq.gz -2 ${pop}_${gen}.R2.fastq.gz -s ${pop}_${gen}.single.fastq.gz
#
#genome=INRA18-TM0523
#gen=g7
#samtools index ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam
#samtools view -hb ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam "gnl|Mygr_323|chr_8" > ${pop}_${gen}.bam
#samtools fastq ${pop}_${gen}.bam -1 ${pop}_${gen}.R1.fastq.gz -2 ${pop}_${gen}.R2.fastq.gz -s ${pop}_${gen}.single.fastq.gz
#
#genome=INRA18-TM0544
#gen=g8
#samtools index ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam
#samtools view -hb ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam "gnl|Mygr_323|chr_8" > ${pop}_${gen}.bam
#samtools fastq ${pop}_${gen}.bam -1 ${pop}_${gen}.R1.fastq.gz -2 ${pop}_${gen}.R2.fastq.gz -s ${pop}_${gen}.single.fastq.gz
#
#genome=INRA18-TM0565
#gen=g9
#samtools index ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam
#samtools view -hb ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam "gnl|Mygr_323|chr_8" > ${pop}_${gen}.bam
#samtools fastq ${pop}_${gen}.bam -1 ${pop}_${gen}.R1.fastq.gz -2 ${pop}_${gen}.R2.fastq.gz -s ${pop}_${gen}.single.fastq.gz
#
#genome=INRA18-TM0585
#gen=g10
#samtools index ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam
#samtools view -hb ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam "gnl|Mygr_323|chr_8" > ${pop}_${gen}.bam
#samtools fastq ${pop}_${gen}.bam -1 ${pop}_${gen}.R1.fastq.gz -2 ${pop}_${gen}.R2.fastq.gz -s ${pop}_${gen}.single.fastq.gz

#######

#path=/work/project/baric/BIOGER/VISA
#genome=INRA19-TM0368
#pop=pop2
#gen=g1
#samtools index ${path}/variant_calling/${genome}/${genome}/samtools/dup.${genome}.sorted.bam
#samtools view -hb ${path}/variant_calling/${genome}/${genome}/samtools/dup.${genome}.sorted.bam "chr_8" > ${pop}_${gen}.bam
#samtools fastq ${pop}_${gen}.bam -1 ${pop}_${gen}.R1.fastq.gz -2 ${pop}_${gen}.R2.fastq.gz -s ${pop}_${gen}.single.fastq.gz
#
#genome=INRA19-TM0384
#gen=g2
#samtools index ${path}/variant_calling/${genome}/${genome}/samtools/dup.${genome}.sorted.bam
#samtools view -hb ${path}/variant_calling/${genome}/${genome}/samtools/dup.${genome}.sorted.bam "chr_8" > ${pop}_${gen}.bam
#samtools fastq ${pop}_${gen}.bam -1 ${pop}_${gen}.R1.fastq.gz -2 ${pop}_${gen}.R2.fastq.gz -s ${pop}_${gen}.single.fastq.gz
#
#genome=INRA19-TM0416
#gen=g3
#samtools index ${path}/variant_calling/${genome}/${genome}/samtools/dup.${genome}.sorted.bam
#samtools view -hb ${path}/variant_calling/${genome}/${genome}/samtools/dup.${genome}.sorted.bam "chr_8" > ${pop}_${gen}.bam
#samtools fastq ${pop}_${gen}.bam -1 ${pop}_${gen}.R1.fastq.gz -2 ${pop}_${gen}.R2.fastq.gz -s ${pop}_${gen}.single.fastq.gz
#
#genome=INRA19-TM0480
#gen=g4
#samtools index ${path}/variant_calling/${genome}/${genome}/samtools/dup.${genome}.sorted.bam
#samtools view -hb ${path}/variant_calling/${genome}/${genome}/samtools/dup.${genome}.sorted.bam "chr_8" > ${pop}_${gen}.bam
#samtools fastq ${pop}_${gen}.bam -1 ${pop}_${gen}.R1.fastq.gz -2 ${pop}_${gen}.R2.fastq.gz -s ${pop}_${gen}.single.fastq.gz
#
#genome=INRA19-TM0499
#gen=g5
#samtools index ${path}/variant_calling/${genome}/${genome}/samtools/dup.${genome}.sorted.bam
#samtools view -hb ${path}/variant_calling/${genome}/${genome}/samtools/dup.${genome}.sorted.bam "chr_8" > ${pop}_${gen}.bam
#samtools fastq ${pop}_${gen}.bam -1 ${pop}_${gen}.R1.fastq.gz -2 ${pop}_${gen}.R2.fastq.gz -s ${pop}_${gen}.single.fastq.gz
#
#genome=INRA19-TM0510
#gen=g6
#samtools index ${path}/variant_calling/${genome}/${genome}/samtools/dup.${genome}.sorted.bam
#samtools view -hb ${path}/variant_calling/${genome}/${genome}/samtools/dup.${genome}.sorted.bam "chr_8" > ${pop}_${gen}.bam
#samtools fastq ${pop}_${gen}.bam -1 ${pop}_${gen}.R1.fastq.gz -2 ${pop}_${gen}.R2.fastq.gz -s ${pop}_${gen}.single.fastq.gz
#
#genome=INRA19-TM0566
#gen=g7
#samtools index ${path}/variant_calling/${genome}/${genome}/samtools/dup.${genome}.sorted.bam
#samtools view -hb ${path}/variant_calling/${genome}/${genome}/samtools/dup.${genome}.sorted.bam "chr_8" > ${pop}_${gen}.bam
#samtools fastq ${pop}_${gen}.bam -1 ${pop}_${gen}.R1.fastq.gz -2 ${pop}_${gen}.R2.fastq.gz -s ${pop}_${gen}.single.fastq.gz
#
#genome=INRA19-TM0690
#gen=g8
#samtools index ${path}/variant_calling/${genome}/${genome}/samtools/dup.${genome}.sorted.bam
#samtools view -hb ${path}/variant_calling/${genome}/${genome}/samtools/dup.${genome}.sorted.bam "chr_8" > ${pop}_${gen}.bam
#samtools fastq ${pop}_${gen}.bam -1 ${pop}_${gen}.R1.fastq.gz -2 ${pop}_${gen}.R2.fastq.gz -s ${pop}_${gen}.single.fastq.gz
#
#genome=INRA19-TM0714
#gen=g9
#samtools index ${path}/variant_calling/${genome}/${genome}/samtools/dup.${genome}.sorted.bam
#samtools view -hb ${path}/variant_calling/${genome}/${genome}/samtools/dup.${genome}.sorted.bam "chr_8" > ${pop}_${gen}.bam
#samtools fastq ${pop}_${gen}.bam -1 ${pop}_${gen}.R1.fastq.gz -2 ${pop}_${gen}.R2.fastq.gz -s ${pop}_${gen}.single.fastq.gz
#
#genome=INRA19-TM0807
#gen=g10
#samtools index ${path}/variant_calling/${genome}/${genome}/samtools/dup.${genome}.sorted.bam
#samtools view -hb ${path}/variant_calling/${genome}/${genome}/samtools/dup.${genome}.sorted.bam "chr_8" > ${pop}_${gen}.bam
#samtools fastq ${pop}_${gen}.bam -1 ${pop}_${gen}.R1.fastq.gz -2 ${pop}_${gen}.R2.fastq.gz -s ${pop}_${gen}.single.fastq.gz

#######

path=/work/project/baric/BIOGER/TEAGASC_2022
genome=S19.2.1
pop=pop3
gen=g1
samtools index ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam
samtools view -hb ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam "gnl|Mygr_323|chr_8" > ${pop}_${gen}.bam
samtools fastq ${pop}_${gen}.bam -1 ${pop}_${gen}.R1.fastq.gz -2 ${pop}_${gen}.R2.fastq.gz -s ${pop}_${gen}.single.fastq.gz

genome=S19.2.5
gen=g2
samtools index ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam
samtools view -hb ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam "gnl|Mygr_323|chr_8" > ${pop}_${gen}.bam
samtools fastq ${pop}_${gen}.bam -1 ${pop}_${gen}.R1.fastq.gz -2 ${pop}_${gen}.R2.fastq.gz -s ${pop}_${gen}.single.fastq.gz

genome=S19.2.8
gen=g3
samtools index ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam
samtools view -hb ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam "gnl|Mygr_323|chr_8" > ${pop}_${gen}.bam
samtools fastq ${pop}_${gen}.bam -1 ${pop}_${gen}.R1.fastq.gz -2 ${pop}_${gen}.R2.fastq.gz -s ${pop}_${gen}.single.fastq.gz

genome=S19.3.1
gen=g4
samtools index ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam
samtools view -hb ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam "gnl|Mygr_323|chr_8" > ${pop}_${gen}.bam
samtools fastq ${pop}_${gen}.bam -1 ${pop}_${gen}.R1.fastq.gz -2 ${pop}_${gen}.R2.fastq.gz -s ${pop}_${gen}.single.fastq.gz

genome=S19.3.7
gen=g5
samtools index ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam
samtools view -hb ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam "gnl|Mygr_323|chr_8" > ${pop}_${gen}.bam
samtools fastq ${pop}_${gen}.bam -1 ${pop}_${gen}.R1.fastq.gz -2 ${pop}_${gen}.R2.fastq.gz -s ${pop}_${gen}.single.fastq.gz

genome=S19.4.3
gen=g6
samtools index ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam
samtools view -hb ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam "gnl|Mygr_323|chr_8" > ${pop}_${gen}.bam
samtools fastq ${pop}_${gen}.bam -1 ${pop}_${gen}.R1.fastq.gz -2 ${pop}_${gen}.R2.fastq.gz -s ${pop}_${gen}.single.fastq.gz

genome=S19.4.6
gen=g7
samtools index ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam
samtools view -hb ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam "gnl|Mygr_323|chr_8" > ${pop}_${gen}.bam
samtools fastq ${pop}_${gen}.bam -1 ${pop}_${gen}.R1.fastq.gz -2 ${pop}_${gen}.R2.fastq.gz -s ${pop}_${gen}.single.fastq.gz

genome=S19.4.9
gen=g8
samtools index ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam
samtools view -hb ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam "gnl|Mygr_323|chr_8" > ${pop}_${gen}.bam
samtools fastq ${pop}_${gen}.bam -1 ${pop}_${gen}.R1.fastq.gz -2 ${pop}_${gen}.R2.fastq.gz -s ${pop}_${gen}.single.fastq.gz

genome=S19.5.3
gen=g9
samtools index ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam
samtools view -hb ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam "gnl|Mygr_323|chr_8" > ${pop}_${gen}.bam
samtools fastq ${pop}_${gen}.bam -1 ${pop}_${gen}.R1.fastq.gz -2 ${pop}_${gen}.R2.fastq.gz -s ${pop}_${gen}.single.fastq.gz

genome=S19.6.8
gen=g10
samtools index ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam
samtools view -hb ${path}/variant_calling/${genome}/${genome}/bwa/${genome}.sorted.bam "gnl|Mygr_323|chr_8" > ${pop}_${gen}.bam
samtools fastq ${pop}_${gen}.bam -1 ${pop}_${gen}.R1.fastq.gz -2 ${pop}_${gen}.R2.fastq.gz -s ${pop}_${gen}.single.fastq.gz