5. Output files¶
-out
option allows to specify the output directory or the name for the image file (if a single image file is the output).
5.1. Image file (PNG, JPG)¶
By default, the program generates image files in png
format. It is possible to select jpg
format using the -imagetype
option.
$ bamsnap \
-bam ./data/NA12878.bam \
-pos chr10:117542948 \
-out ./out/NA12878_chr10_117542948.jpg \
-imagetype jpg \
-save_image_only
Note
To save only snap image files, use the -save_image_only
option.
Inside the output directory, images are saved in a default sub-directory. It is possible to rename this folder using the the -image_dir_name
option.
$ bamsnap \
-bam ./data/NA12879.bam \
-vcf ./data/NATRIO_test_3.vcf \
-out ./out/NATRIO_test_3 \
-image_dir_name test_images
This example creates ./out/NATRIO_test_3/test_images
folder that contains the generated snap image files.
By default, the program generates a single plot file for multiple bam files. -separated_bam
option allows to generate a plot file for each of the bam files.
5.2. Compressed file (-zipout
)¶
It is possible to save a compressed (zip
) output file using the -zipout
option.
$ bamsnap \
-bam ./data/NA12879.bam \
-vcf ./data/NATRIO_test_3.vcf \
-out ./out/NATRIO_test_3 \
-save_image_only \
-zipout
This example creates ./out/NATRIO_test_3.zip
file.
5.3. HTML file (index html)¶
If -save_image_only
is not used, index.html is generated by default.