gistfile1.sh

#!/bin/bash
#

#$coverage_bin -in $a_out_bin -ia $hsap_ref -od $plots_dir -cg #-u
mosaik_dir="$HOME/mosaik/bin"
build_bin="$mosaik_dir/MosaikBuild"
align_bin="$mosaik_dir/MosaikAligner"
text_bin="$mosaik_dir/MosaikText"
jump_bin="$mosaik_dir/MosaikJump"
coverage_bin="$mosaik_dir/MosaikCoverage"

data_dir="/mnt/454"
#reads="$data_dir/reads/reads.fna"
#quals="$data_dir/reads/qualities.fna"
reads="$data_dir/reads/one_region.fna"
quals="$data_dir/reads/one_region.fna"
reads_bin="$data_dir/reads/one_region_454_hsap_reads.dat"
hsap_ref="$HOME/mosaik/hsap/full_hsap.dat"
cpus=8
jump_database="$HOME/mosaik/hsap/hsap_jump_15"
a_out_bin="$data_dir/mapping_out/hsap_aligned.dat"
hash_size=15
plots_dir="$data_dir/plots"

# 1. Build ref
build_ref() 
{
  $build_bin -fr full_hsap.fa -oa full_hsap.dat
}

# 2. Convert reads
convert_reads()
{
  $build_bin -fr $reads -fq $quals -out $reads_bin -st 454
}

# 3. create the jump database (will keep the keys file in memory)
create_jump()
{
  $jump_bin -ia $hsap_ref -out $jump_database -hs $hash_size -km
}

# 4. Align the reads
align() 
{
  $align_bin \
  -in $reads_bin \
  -out $a_out_bin \
  -ia $hsap_ref \
  -hs $hash_size \
  -mmp .05 \
  -a all \
  -m all \
  -mhp 100 \
  -act 26 \
  -j $jump_database \
  -km -pm \
  -p $cpus
}

# 5. extract mapping info to screen
to_screen()
{
  $text_bin -in $a_out_bin -screen # -u
}

# report coverage
plots()
{
  mkdir -p $plots_dir
  $coverage_bin -in $a_out_bin -ia $hsap_ref -od $plots_dir -cg #-u
}

plots