%%bash
java -Xmx4G -jar ../utilities/pilon-1.10.jar \
                --genome ../data/RM8375/ref/CFSAN008157.HGAP.fasta \
                --frags ../analysis/bioinf/sequence_purity/mapping/SRR1555296.bam \
                --changes --vcf --tracks \
                --fix "all" --debug #note --fix "all" default

"""
Explanation: Testing out Pilon
Objective: Test out using Pilon on the MiSeq and PGM data
Approach: Running Pilon using bash commands, evaluate revise reference relative to HGAP and GenBank LT2
Testing single paried end dataset
End of explanation
"""


%%bash 
python ../analysis/bioinf/sequence_purity/run_bwa_mem_pe.py \
        ../analysis/bioinf/sequence_purity/bwa_mem_pipeline_params.txt

"""
Explanation: Error with head, needed to rerun bwa with revised params file
Error with memory allocation, not sure if too many applicaitons running on laptop, or docker memory restrictions
* re-running after closing windows and restarting finder (hung up on moving files to trash)
* Need to look into changing amount of memory allocated to ipython notebook
End of explanation
"""


At 

%%bash
ls ../data/RM8375/PGM/bam/*bam >HGAP.PGM.bams
samtools merge -b HGAP.PGM.bams HGAP_PGM.bam
samtools index HGAP_PGM.bam

"""
Explanation: Merging bams
End of explanation
"""


