---
title: "05-Variants"
format: html
editor: visual
excute: 
  warnings: false
  message: false
  echo: false
---

5/6/2025 Objective: Download alignment files, visualize IGV, and potentially display two feature files

```{r}
## check directory
getwd()
```

```{r, engine='bash'}
## change directory then call on each alignment file: 19F and Virginica 
cd /assignments/data
curl -O https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/19F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam 
curl -O https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/19F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai

{r, engine='bash'}          
cd /assignments/data/ 
curl -O https://gannet.fish.washington.edu/seashell/bu-mox/data/Cvirg-genome/GCF_002022765.2_C_virginica-3.0_genomic.fa 
curl -O https://gannet.fish.washington.edu/seashell/bu-mox/data/Cvirg-genome/GCF_002022765.2_C_virginica-3.0_genomic.fa.fai
```

```{r}
## apply following code in terminal; Directs samtools to view the documents stored in the data folder directory -- specifically specified below

#NOTE: 1_bismark is your BAM and Virginica is your fasta file

/home/shared/samtools-1.12/samtools \
tview assignments/data/19F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam \
GCF_002022765.2_C_virginica-3.0_genomic.fa
```

```{r, engine='bash'}
## use absolute path directory. F143 fasta file into the data directory

cd /home/shared/8TB_HDD_02/cberry1/Claudia-Halibut/assignments/data
curl -O https://owl.fish.washington.edu/nightingales/C_gigas/F143n08_R2_001.fastq.gz
curl -O https://owl.fish.washington.edu/nightingales/C_gigas/F143n08_R1_001.fastq.gz

```

```{r, engine='bash'}
## transfer Roslin data [curl()] via URL **add visualization?**

cd /home/shared/8TB_HDD_02/cberry1/Claudia-Halibut/assignments/data
curl -O https://gannet.fish.washington.edu/panopea/Cg-roslin/cgigas_uk_roslin_v1_genomic-mito.fa 
curl -O https://gannet.fish.washington.edu/panopea/Cg-roslin/cgigas_uk_roslin_v1_genomic-mito.fa.fai
curl -O https://gannet.fish.washington.edu/panopea/Cg-roslin/GCF_902806645.1_cgigas_uk_roslin_v1_genomic-mito.gtf
```

```{r, engine='bash'}
cd /home/shared/8TB_HDD_02/cberry1/Claudia-Halibut

/home/shared/hisat2-2.2.1/hisat2-build \
  assignments/data/cgigas_uk_roslin_v1_genomic-mito.fa assignments/output/cgigas_uk_roslin_v1_genomic-mito.index
```

```{r}
getwd()
```

```{r, engine='bash'}
#NOTE: example reference for creating variable that shortens directory links

#WORK_DIR=/home/shared/8TB_HDD_02/cberry1/Claudia-Halibut/assignments
#echo "Moving into ${WORK_DIR}"
#cd $WORK_DIR

#/home/shared/hisat2-2.2.1/hisat2 \
#      $WORK_DIR/output/cgigas_uk_roslin_v1_genomic-mito.index\
#     -p 4 -1 $WORK_DIR/data/F143n08_R1_001.fastq.gz\
#     -2 $WORK_DIR/data/F143n08_R2_001.fastq.gz\
#     -S $WORK_DIR/output/F143_cgigas.sam

#tail -1 output/F143_cgigas.sam
```

```{r, engine='bash'}
## keep in mind that every line of code resets to changed directory; the computer isn't that smart. While cd() is not necessary it was added for assurance

## call on the alignment file in the output directory,launch selected threads from the file information in desired document located in data directory, write SAM alignment to the F143 (-S) -- then print the last line 
cd /home/shared/8TB_HDD_02/cberry1/Claudia-Halibut/assignments

/home/shared/hisat2-2.2.1/hisat2 \
      output/cgigas_uk_roslin_v1_genomic-mito.index\
     -p 4 -1 data/F143n08_R1_001.fastq.gz\
     -2 data/F143n08_R2_001.fastq.gz\
    -S output/F143_cgigas.sam

tail -1 output/F143_cgigas.sam
```

```{r, engine='bash'}
# Convert SAM to BAM, using 4 additional threads - fix later (as of 4/08/2025 3PM)
/home/shared/samtools-1.12/samtools view -@ 4 -bS \
../output/F143_cgigas.sam > ../output/F143_cgigas.bam
```

```{r, engine='bash'}
# Sort the BAM file, using 4 additional threads
/home/shared/samtools-1.12/samtools sort -@ 4 \
../output/F143_cgigas.bam -o ../output/F143_cgigas_sorted.bam

# Index the sorted BAM file (multi-threading is not applicable to this operation)
/home/shared/samtools-1.12/samtools index \
../output/F143_cgigas_sorted.bam

## genome viewer for future code -- remember how 
```