Joel Kalior

## minimap seq identity
#!/bin/bash

PREFIX1=$1
PREFIX2=$2
N_FILES=$3

for ((i=0; i < ${N_FILES}; i++))
do
    minimap2 -c  "${PREFIX1}_${i}_0.fastq.gz" "${PREFIX2}_${i}_0.fastq.gz" \
    | perl -ane 'if(/tp:A:P/&&/NM:i:(\d+)/){$n+=$1;$m+=$1 while/(\d+)M/g;$g+=$1,++$o while/(\d+)[ID]/g}END{print(($n-$g+$o)/($m+$o),"\n")}' >> seq_similarity_different_basecalling.log

## keybase.md

      
        
          
            
              
              1 file
            
          
          
            
              
              0 forks
            
          
          
            
              
              0 comments
            
          
          
            
              
              0 stars
            
          
        
        
          
              
          
          
            
                Kalior
                / keybase.md
            
            
              Created
              February 5, 2016 11:55
            
          
        
      
        
  
      
    Keybase proof

I hereby claim:

I am kalior on github.
I am kalior (https://keybase.io/kalior) on keybase.
I have a public key ASDwoGQkCaHDcCjIoRSwHZwfDM4vd1Pglugyi641iFc4vQo

To claim this, I am signing this object:
	#!/bin/bash

	PREFIX1=$1
	PREFIX2=$2
	N_FILES=$3

	for ((i=0; i < ${N_FILES}; i++))
	do
	minimap2 -c "${PREFIX1}_${i}_0.fastq.gz" "${PREFIX2}_${i}_0.fastq.gz" \
	\| perl -ane 'if(/tp:A:P/&&/NM:i:(\d+)/){$n+=$1;$m+=$1 while/(\d+)M/g;$g+=$1,++$o while/(\d+)[ID]/g}END{print(($n-$g+$o)/($m+$o),"\n")}' >> seq_similarity_different_basecalling.log