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Gpu dev #743

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hasindu2008
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Methylation aware polishing has been now implemented for the GPU.

The answers from CPU and GPU for multi-model (-q dam,dcm) now match

The vcf resulted from CPU and GPU for single-model as well as multi-model are attached
polished_.zip

Reference:
ftp://ftp.ensemblgenomes.org/pub/bacteria/release-45/fasta/bacteria_0_collection/escherichia_coli_str_k_12_substr_mg1655/dna/Escherichia_coli_str_k_12_substr_mg1655.ASM584v2.dna.toplevel.fa.gz

Reads:
https://nanopore.s3.climb.ac.uk/Zymo-GridION-EVEN-BB-SN.fq.gz
https://nanopore.s3.climb.ac.uk/Zymo-GridION-EVEN-BB-SN_signal.tar

Commands:

minimap2 -ax map-ont -t32 ecoli_k12_ms1655.fa Zymo-GridION-EVEN-BB-SN.fq > Zymo-GridION-EVEN-BB-SN.sam 
samtools sort  Zymo-GridION-EVEN-BB-SN.sam >  Zymo-GridION-EVEN-BB-SN.bam 
samtools index  Zymo-GridION-EVEN-BB-SN.bam 
~/nanopolish/nanopolish index Zymo-GridION-EVEN-BB-SN.fq -d  Zymo-GridION-EVEN-BB-SN 

 
./nanopolish variants --consensus -o $DATADIR/polished_cpu_single_model.vcf -w "Chromosome:200000-202000" -r $DATADIR/reads.fasta -b $DATADIR/reads.bam -g $DATADIR/draft.fa >  $DATADIR/candidates_cpu_single_model.vcf 
 ./nanopolish variants --consensus -o $DATADIR/polished_gpu_single_model.vcf -w "Chromosome:200000-202000" -r $DATADIR/reads.fasta -b $DATADIR/reads.bam -g $DATADIR/draft.fa --gpu=1 > $DATADIR/candidates_gpu_single_model.vcf 
./nanopolish variants --consensus -o $DATADIR/polished_cpu_multi_model.vcf -w "Chromosome:200000-202000" -r $DATADIR/reads.fasta -b $DATADIR/reads.bam -g $DATADIR/draft.fa   -q dcm,dam  > $DATADIR/candidates_cpu_multi_model.vcf 
./nanopolish variants --consensus -o $DATADIR/polished_gpu_multi_model.vcf -w "Chromosome:200000-202000" -r $DATADIR/reads.fasta -b $DATADIR/reads.bam -g $DATADIR/draft.fa --gpu=1  -q dcm,dam > $DATADIR/candidates_gpu_multi_model.vcf

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