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|
#!/usr/bin/env bash
# test-gbwt.sh: Plot the effect of haplotype information on mapping performance
# We are going to compare 5 mapping regimes:
# 1. The snp1kg graph without the variants in the sample (negative control)
# 2. The full snp1kg graph (Heng Effect positive control)
# 3. The full snp1kg graph with GBWT haplotype information (under test)
# 4. The frequency-filtered minaf snp1kg graph (current best)
# 5. The primary path graph (Heng Effect negative control)
# We want to know if the GBWT reduces the Heng Effect (poor mapping due to
# spurious alignments to rare variants)
# OK so on to the actual code.
set -ex
# Define constants
# Define a region name to process. This sets the name that the graphs and
# indexes will be saved/looked for under.
REGION_NAME="CHR21"
# Define the VCF and FASTA basenames. We assume the VCF has a TBI.
VCF_BASENAME="1kg_hg19-CHR21.vcf.gz"
FASTA_BASENAME="CHR21.fa"
# Define where to get them
SOURCE_BASE_URL="s3://vg-data/bakeoff"
# Define the contig we are using
GRAPH_CONTIG="21"
# Define the region to build the graph on, as contig[:start-end]
GRAPH_REGION="${GRAPH_CONTIG}"
# Set a FASTQ to model reads after
TRAINING_FASTQ="ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/NA12878/NIST_NA12878_HG001_HiSeq_300x/131219_D00360_005_BH814YADXX/Project_RM8398/Sample_U5a/U5a_AGTCAA_L002_R1_007.fastq.gz"
# And a read simulation seed
READ_SEED="90"
# And a read count
READ_COUNT="10000000"
# Chunks to simulate in (which affects results)
READ_CHUNKS="32"
MODE="21"
if [[ "${MODE}" == "mhc" ]]; then
# Actually do a smaller test
READ_COUNT="100000"
REGION_NAME="MHC"
GRAPH_CONTIG="6"
GRAPH_REGION="${GRAPH_CONTIG}:28510119-33480577"
FASTA_BASENAME="chr6.fa.gz"
VCF_BASENAME="1kg_hg38-MHC.vcf.gz"
elif [[ "${MODE}" == "tiny" ]]; then
# Do just 20 kb of MHC and a very few reads
READ_COUNT="1000"
REGION_NAME="MHC"
GRAPH_CONTIG="6"
GRAPH_REGION="${GRAPH_CONTIG}:28510119-28520119"
FASTA_BASENAME="chr6.fa.gz"
VCF_BASENAME="1kg_hg38-MHC.vcf.gz"
fi
# Define the sample to use for synthesizing reads
SAMPLE_NAME="HG00096"
# What min allele frequency limit do we use?
MIN_AF="0.0335570469"
# Do we actually want to run the mapeval jobs? Or just do plotting?
RUN_JOBS="1"
# Now we need to parse our arguments
usage() {
# Print usage to stderr
exec 1>&2
printf "Usage: $0 [Options] TREE_PATH GRAPHS_PATH OUTPUT_PATH\n"
printf "\tTREE_PATH\ta Toil job tree location\n"
printf "\tGRAPHS_PATH\ta directory of graphs (which, if extant, allows graph construction to be skipped)\n"
printf "\tOUTPUT_PATH\ta results directory\n"
exit 1
}
while getopts "" o; do
case "${o}" in
*)
usage
;;
esac
done
shift $((OPTIND-1))
if [[ "$#" -lt "3" ]]; then
# Too few arguments
usage
fi
TREE_PATH="${1}"
shift
GRAPHS_PATH="${1}"
shift
OUTPUT_PATH="${1}"
shift
if [[ -e "${TREE_PATH}" ]]; then
# Make sure we don't clobber the first arg on accident
echo "ERROR: Tree path ${TREE_PATH} already exists and needs to be removed" 1>&2
exit 1
fi
mkdir -p "${TREE_PATH}"
# Generate a toil-vg config
toil-vg generate-config > "${TREE_PATH}/toil-vg.conf"
sed -i "s/alignment-cores:.*/alignment-cores: 64/" "${TREE_PATH}/toil-vg.conf"
sed -i "s/alignment-disk:.*/alignment-disk: '20G'/" "${TREE_PATH}/toil-vg.conf"
# Now we need to make sure our graphs exist and are downloaded
if [[ ! -d "${GRAPHS_PATH}" ]]; then
# Graphs need to be gotten
if [[ -e "${GRAPHS_PATH}" ]]; then
# It needs to not exist at all
echo "ERROR: Graph path ${GRAPHS_PATH} is not a directory" 1>&2
exit 1
fi
# Make the directory
mkdir -p "${GRAPHS_PATH}"
# Construct the graphs
# Hardcoded constants here go with the snp1kg URLs above.
toil-vg construct "${TREE_PATH}/construct" "${GRAPHS_PATH}" \
--config "${TREE_PATH}/toil-vg.conf" \
--vcf "${SOURCE_BASE_URL}/${VCF_BASENAME}" \
--fasta "${SOURCE_BASE_URL}/${FASTA_BASENAME}" \
--out_name "snp1kg-${REGION_NAME}" \
--alt_paths \
--realTimeLogging \
--control_sample "${SAMPLE_NAME}" \
--haplo_sample "${SAMPLE_NAME}" \
--filter_samples "${SAMPLE_NAME}" \
--regions "${GRAPH_REGION}" \
--min_af "${MIN_AF}" \
--primary \
--gcsa_index \
--xg_index \
--gbwt_index \
--snarls_index
fi
READS_DIR="${GRAPHS_PATH}/sim-${READ_SEED}-${READ_COUNT}-${READ_CHUNKS}"
if [[ ! -e "${READS_DIR}" ]]; then
# Now we need to simulate reads from the two haplotypes
# This will make a "sim.gam"
toil-vg sim "${TREE_PATH}/sim" \
"${GRAPHS_PATH}/snp1kg-${REGION_NAME}_${SAMPLE_NAME}_haplo_thread_0.xg" \
"${GRAPHS_PATH}/snp1kg-${REGION_NAME}_${SAMPLE_NAME}_haplo_thread_1.xg" \
"${READ_COUNT}" \
"${READS_DIR}" \
--config "${TREE_PATH}/toil-vg.conf" \
--annotate_xg "${GRAPHS_PATH}/snp1kg-${REGION_NAME}_${SAMPLE_NAME}_haplo.xg" \
--gam \
--fastq_out \
--seed "${READ_SEED}" \
--sim_chunks "${READ_CHUNKS}" \
--fastq "${TRAINING_FASTQ}"
fi
# Make sure we have the SLLS linear index file
# We will work on the filtered VCF
FILTERED_VCF_BASENAME="${VCF_BASENAME%.vcf.gz}_filter.vcf.gz"
SLLS_INDEX="${GRAPHS_PATH}/slls/${FILTERED_VCF_BASENAME}.slls"
if [[ ! -e "${SLLS_INDEX}" ]]; then
# We need to make the SLLS index
mkdir "${GRAPHS_PATH}/slls"
cp "${GRAPHS_PATH}/${FILTERED_VCF_BASENAME}" "${GRAPHS_PATH}/slls/${FILTERED_VCF_BASENAME}"
cd deps/sublinear-Li-Stephens && make && cd ../..
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:`pwd`/deps/sublinear-Li-Stephens/deps/htslib/ ./deps/sublinear-Li-Stephens/bin/serializer "${GRAPHS_PATH}/slls/${FILTERED_VCF_BASENAME}"
fi
# Now we do a bunch of stuff in parallel
JOB_ARRAY=()
# What do they return?
JOB_RETURNS=()
# What condition names have we run
CONDITIONS=()
# How many jobs should we let run at once
MAX_JOBS=2
# We have a function to wait for the parallel jobs to finish, if MAX_JOBS or
# more are running
function wait_on_jobs() {
# How many jobs are running?
CURRENT_JOBS="${#JOB_ARRAY[@]}"
if [[ "${CURRENT_JOBS}" -lt "${MAX_JOBS}" ]]; then
# If we haven't hit the cap, don't do anything.
return
fi
# Otherwise we have to collect some jobs
COLLECTED_JOBS=0
# Now wait for all the jobs and fail if any failed
for JOB in "${JOB_ARRAY[@]}"; do
if [[ -z "${JOB}" ]]; then
# Drop empty strings that get in here. This happens if we forget
# the trailing & on something intended to be in parallel.
continue
fi
wait "${JOB}"
RETURN_CODE="$?"
if [[ "${RETURN_CODE}" != "0" ]]; then
# A job has failed.
# Collect up all the jobs now, actually.
echo "Job PID ${JOB} failed with return code ${RETURN_CODE}; flushing queue" 1>&2
MAX_JOBS=0
fi
JOB_RETURNS+=("${RETURN_CODE}")
((COLLECTED_JOBS+=1))
if [[ "$((CURRENT_JOBS-COLLECTED_JOBS))" -lt "${MAX_JOBS}" ]]; then
# No need to clean up any more jobs
break
fi
done
JOB_NUMBER=1
for JOB_RETURN in "${JOB_RETURNS[@]}"; do
echo "Job ${JOB_NUMBER} exit status: ${JOB_RETURN}"
((JOB_NUMBER+=1))
if [[ "${JOB_RETURN}" != "0" ]]; then
echo "Job failed!" 1>&2
exit 1
fi
done
# Pop off the finished jobs
JOB_ARRAY=("${JOB_ARRAY[@]:${COLLECTED_JOBS}}")
# Delete all the return codes
JOB_RETURNS=()
}
if [[ "${RUN_JOBS}" == "1" ]]; then
# We actually want to run the toil-vg jobs
#CONDITIONS+=("snp1kg-mp")
#if [[ ! -e "${OUTPUT_PATH}/snp1kg-mp" ]]; then
# # Do the full snp1kg graph multipath
# toil-vg mapeval "${TREE_PATH}/snp1kg-mp" "${OUTPUT_PATH}/snp1kg-mp" \
# --single_reads_chunk \
# --config "${TREE_PATH}/toil-vg.conf" \
# --maxDisk 100G \
# --multipath-only \
# --fastq "${READS_DIR}/sim.fq.gz" \
# --truth "${READS_DIR}/true.pos" \
# --index-bases "${GRAPHS_PATH}/snp1kg-${REGION_NAME}_filter" \
# --gam-names snp1kg 2>&1 &
# JOB_ARRAY+=("$!")
#fi
#wait_on_jobs
CONDITIONS+=("snp1kg-mp-snarlcut")
if [[ ! -e "${OUTPUT_PATH}/snp1kg-mp-snarlcut" ]]; then
# Do the full snp1kg graph multipath
toil-vg mapeval "${TREE_PATH}/snp1kg-mp-snarlcut" "${OUTPUT_PATH}/snp1kg-mp-snarlcut" \
--single_reads_chunk \
--config "${TREE_PATH}/toil-vg.conf" \
--maxDisk 100G \
--multipath-only \
--use-snarls \
--fastq "${READS_DIR}/sim.fq.gz" \
--truth "${READS_DIR}/true.pos" \
--index-bases "${GRAPHS_PATH}/snp1kg-${REGION_NAME}_filter" \
--gam-names snp1kg-snarlcut 2>&1 &
JOB_ARRAY+=("$!")
fi
wait_on_jobs
#CONDITIONS+=("snp1kg-mp-gbwt")
#if [[ ! -e "${OUTPUT_PATH}/snp1kg-mp-gbwt" ]]; then
# # Do the full snp1kg graph multipath with gbwt
# toil-vg mapeval "${TREE_PATH}/snp1kg-mp-gbwt" "${OUTPUT_PATH}/snp1kg-mp-gbwt" \
# --single_reads_chunk \
# --config "${TREE_PATH}/toil-vg.conf" \
# --maxDisk 100G \
# --multipath-only \
# --use-gbwt \
# --fastq "${READS_DIR}/sim.fq.gz" \
# --truth "${READS_DIR}/true.pos" \
# --index-bases "${GRAPHS_PATH}/snp1kg-${REGION_NAME}_filter" \
# --gam-names snp1kg-gbwt 2>&1 &
# JOB_ARRAY+=("$!")
#fi
#wait_on_jobs
#CONDITIONS+=("snp1kg-mp-gbwt-traceback")
#if [[ ! -e "${OUTPUT_PATH}/snp1kg-mp-gbwt-traceback" ]]; then
# # Do the full snp1kg graph multipath with gbwt
# toil-vg mapeval "${TREE_PATH}/snp1kg-mp-gbwt-traceback" "${OUTPUT_PATH}/snp1kg-mp-gbwt-traceback" \
# --single_reads_chunk \
# --config "${TREE_PATH}/toil-vg.conf" \
# --maxDisk 100G \
# --multipath-only \
# --use-gbwt \
# --mpmap_opts "--max-paths 10" \
# --fastq "${READS_DIR}/sim.fq.gz" \
# --truth "${READS_DIR}/true.pos" \
# --index-bases "${GRAPHS_PATH}/snp1kg-${REGION_NAME}_filter" \
# --gam-names snp1kg-gbwt-traceback 2>&1 &
# JOB_ARRAY+=("$!")
#fi
#wait_on_jobs
CONDITIONS+=("snp1kg-mp-gbwt-snarlcut")
if [[ ! -e "${OUTPUT_PATH}/snp1kg-mp-gbwt-snarlcut" ]]; then
# Do the full snp1kg graph multipath with snarl cutting and gbwt but single path traceback
toil-vg mapeval "${TREE_PATH}/snp1kg-mp-gbwt-snarlcut" "${OUTPUT_PATH}/snp1kg-mp-gbwt-snarlcut" \
--single_reads_chunk \
--config "${TREE_PATH}/toil-vg.conf" \
--maxDisk 100G \
--multipath-only \
--use-gbwt \
--use-snarls \
--fastq "${READS_DIR}/sim.fq.gz" \
--truth "${READS_DIR}/true.pos" \
--index-bases "${GRAPHS_PATH}/snp1kg-${REGION_NAME}_filter" \
--gam-names snp1kg-gbwt-snarlcut 2>&1 &
JOB_ARRAY+=("$!")
fi
wait_on_jobs
CONDITIONS+=("snp1kg-mp-gbwt-traceback-snarlcut")
if [[ ! -e "${OUTPUT_PATH}/snp1kg-mp-gbwt-traceback-snarlcut" ]]; then
# Do the full snp1kg graph multipath with gbwt
toil-vg mapeval "${TREE_PATH}/snp1kg-mp-gbwt-traceback-snarlcut" "${OUTPUT_PATH}/snp1kg-mp-gbwt-traceback-snarlcut" \
--single_reads_chunk \
--config "${TREE_PATH}/toil-vg.conf" \
--maxDisk 100G \
--multipath-only \
--use-gbwt \
--use-snarls \
--mpmap_opts "--max-paths 10" \
--fastq "${READS_DIR}/sim.fq.gz" \
--truth "${READS_DIR}/true.pos" \
--index-bases "${GRAPHS_PATH}/snp1kg-${REGION_NAME}_filter" \
--gam-names snp1kg-gbwt-traceback-snarlcut 2>&1 &
JOB_ARRAY+=("$!")
fi
wait_on_jobs
# This should replicate our best known performance...
CONDITIONS+=("snp1kg-mp-gbwt-traceback-snarlcut-unfiltered")
if [[ ! -e "${OUTPUT_PATH}/snp1kg-mp-gbwt-traceback-snarlcut-unfiltered" ]]; then
# Do the full snp1kg graph multipath with gbwt
toil-vg mapeval "${TREE_PATH}/snp1kg-mp-gbwt-traceback-snarlcut-unfiltered" "${OUTPUT_PATH}/snp1kg-mp-gbwt-traceback-snarlcut-unfiltered" \
--single_reads_chunk \
--config "${TREE_PATH}/toil-vg.conf" \
--maxDisk 100G \
--multipath-only \
--use-gbwt \
--use-snarls \
--mpmap_opts "--max-paths 10" \
--fastq "${READS_DIR}/sim.fq.gz" \
--truth "${READS_DIR}/true.pos" \
--index-bases "${GRAPHS_PATH}/snp1kg-${REGION_NAME}" \
--gam-names snp1kg-gbwt-traceback-snarlcut-unfiltered 2>&1 &
JOB_ARRAY+=("$!")
fi
wait_on_jobs
CONDITIONS+=("snp1kg-mp-gbwt-traceback")
if [[ ! -e "${OUTPUT_PATH}/snp1kg-mp-gbwt-traceback" ]]; then
# Do the full snp1kg graph multipath with gbwt
toil-vg mapeval "${TREE_PATH}/snp1kg-mp-gbwt-traceback" "${OUTPUT_PATH}/snp1kg-mp-gbwt-traceback" \
--single_reads_chunk \
--config "${TREE_PATH}/toil-vg.conf" \
--maxDisk 100G \
--multipath-only \
--use-gbwt \
--use-snarls \
--mpmap_opts "--max-paths 10" \
--fastq "${READS_DIR}/sim.fq.gz" \
--truth "${READS_DIR}/true.pos" \
--index-bases "${GRAPHS_PATH}/snp1kg-${REGION_NAME}_filter" \
--gam-names snp1kg-gbwt-traceback 2>&1 &
JOB_ARRAY+=("$!")
fi
wait_on_jobs
CONDITIONS+=("snp1kg-mp-minaf-snarlcut")
if [[ ! -e "${OUTPUT_PATH}/snp1kg-mp-minaf-snarlcut" ]]; then
# And with the min allele frequency
toil-vg mapeval "${TREE_PATH}/snp1kg-mp-minaf-snarlcut" "${OUTPUT_PATH}/snp1kg-mp-minaf-snarlcut" \
--single_reads_chunk \
--config "${TREE_PATH}/toil-vg.conf" \
--maxDisk 100G \
--multipath-only \
--use-snarls \
--fastq "${READS_DIR}/sim.fq.gz" \
--truth "${READS_DIR}/true.pos" \
--index-bases "${GRAPHS_PATH}/snp1kg-${REGION_NAME}_minaf_${MIN_AF}" \
--gam-names snp1kg-minaf-snarlcut 2>&1 &
JOB_ARRAY+=("$!")
fi
wait_on_jobs
CONDITIONS+=("snp1kg-mp-minaf")
if [[ ! -e "${OUTPUT_PATH}/snp1kg-mp-minaf" ]]; then
# And with the min allele frequency
toil-vg mapeval "${TREE_PATH}/snp1kg-mp-minaf" "${OUTPUT_PATH}/snp1kg-mp-minaf" \
--single_reads_chunk \
--config "${TREE_PATH}/toil-vg.conf" \
--maxDisk 100G \
--multipath-only \
--use-snarls \
--fastq "${READS_DIR}/sim.fq.gz" \
--truth "${READS_DIR}/true.pos" \
--index-bases "${GRAPHS_PATH}/snp1kg-${REGION_NAME}_minaf_${MIN_AF}" \
--gam-names snp1kg-minaf 2>&1 &
JOB_ARRAY+=("$!")
fi
wait_on_jobs
CONDITIONS+=("snp1kg-mp-positive-snarlcut")
if [[ ! -e "${OUTPUT_PATH}/snp1kg-mp-positive-snarlcut" ]]; then
# And the positive control with only real variants
toil-vg mapeval "${TREE_PATH}/snp1kg-mp-positive-snarlcut" "${OUTPUT_PATH}/snp1kg-mp-positive-snarlcut" \
--single_reads_chunk \
--config "${TREE_PATH}/toil-vg.conf" \
--maxDisk 100G \
--multipath-only \
--use-snarls \
--fastq "${READS_DIR}/sim.fq.gz" \
--truth "${READS_DIR}/true.pos" \
--index-bases "${GRAPHS_PATH}/snp1kg-${REGION_NAME}_${SAMPLE_NAME}" \
--gam-names snp1kg-positive-snarlcut 2>&1 &
JOB_ARRAY+=("$!")
fi
wait_on_jobs
CONDITIONS+=("snp1kg-mp-positive")
if [[ ! -e "${OUTPUT_PATH}/snp1kg-mp-positive" ]]; then
# And the positive control with only real variants
toil-vg mapeval "${TREE_PATH}/snp1kg-mp-positive" "${OUTPUT_PATH}/snp1kg-mp-positive" \
--single_reads_chunk \
--config "${TREE_PATH}/toil-vg.conf" \
--maxDisk 100G \
--multipath-only \
--use-snarls \
--fastq "${READS_DIR}/sim.fq.gz" \
--truth "${READS_DIR}/true.pos" \
--index-bases "${GRAPHS_PATH}/snp1kg-${REGION_NAME}_${SAMPLE_NAME}" \
--gam-names snp1kg-positive 2>&1 &
JOB_ARRAY+=("$!")
fi
wait_on_jobs
CONDITIONS+=("primary-mp-snarlcut")
if [[ ! -e "${OUTPUT_PATH}/primary-mp-snarlcut" ]]; then
# And the primary path only
toil-vg mapeval "${TREE_PATH}/primary-mp-snarlcut" "${OUTPUT_PATH}/primary-mp-snarlcut" \
--single_reads_chunk \
--config "${TREE_PATH}/toil-vg.conf" \
--maxDisk 100G \
--multipath-only \
--use-snarls \
--fastq "${READS_DIR}/sim.fq.gz" \
--truth "${READS_DIR}/true.pos" \
--index-bases "${GRAPHS_PATH}/primary" \
--gam-names primary-snarlcut 2>&1 &
JOB_ARRAY+=("$!")
fi
wait_on_jobs
CONDITIONS+=("primary-mp")
if [[ ! -e "${OUTPUT_PATH}/primary-mp" ]]; then
# And the primary path only
toil-vg mapeval "${TREE_PATH}/primary-mp" "${OUTPUT_PATH}/primary-mp" \
--single_reads_chunk \
--config "${TREE_PATH}/toil-vg.conf" \
--maxDisk 100G \
--multipath-only \
--use-snarls \
--fastq "${READS_DIR}/sim.fq.gz" \
--truth "${READS_DIR}/true.pos" \
--index-bases "${GRAPHS_PATH}/primary" \
--gam-names primary 2>&1 &
JOB_ARRAY+=("$!")
fi
wait_on_jobs
#CONDITIONS+=("snp1kg-mp-slls")
#if [[ ! -e "${OUTPUT_PATH}/snp1kg-mp-slls/position.results.tsv" ]]; then
# # This one's a bit different since we need to manually do the mapping
# if [[ ! -e "${OUTPUT_PATH}/snp1kg-mp-slls/aligned-snp1kg-slls-pe_default.gam" ]]; then
# mkdir -p "${OUTPUT_PATH}/snp1kg-mp-slls"
# vg mpmap --linear-index "${SLLS_INDEX}" \
# --linear-path "${GRAPH_CONTIG}" \
# -x "${GRAPHS_PATH}/snp1kg-${REGION_NAME}_filter.xg" \
# -g "${GRAPHS_PATH}/snp1kg-${REGION_NAME}_filter.gcsa" \
# --fastq "${READS_DIR}/sim.fq.gz" \
# -i \
# -S \
# -t 32 \
# >"${OUTPUT_PATH}/snp1kg-mp-slls/aligned-snp1kg-slls-pe_default.gam"
# fi
# # Then do the mapeval
# toil-vg mapeval "${TREE_PATH}/snp1kg-mp-slls" "${OUTPUT_PATH}/snp1kg-mp-slls" \
# --gams "${OUTPUT_PATH}/snp1kg-mp-slls/aligned-snp1kg-slls-pe_default.gam" \
# --config "${TREE_PATH}/toil-vg.conf" \
# --maxDisk 100G \
# --truth "${READS_DIR}/true.pos" \
# --index-bases "${GRAPHS_PATH}/snp1kg-${REGION_NAME}_filter" \
# --gam-names snp1kg-slls-mp-pe 2>&1 &
# JOB_ARRAY+=("$!")
#fi
#wait_on_jobs
#CONDITIONS+=("snp1kg-mp-slls-snarlcut")
#if [[ ! -e "${OUTPUT_PATH}/snp1kg-mp-slls-snarlcut/position.results.tsv" ]]; then
# # This one's a bit different since we need to manually do the mapping
# if [[ ! -e "${OUTPUT_PATH}/snp1kg-mp-slls-snarlcut/aligned-snp1kg-slls-snarlcut-pe_default.gam" ]]; then
# mkdir -p "${OUTPUT_PATH}/snp1kg-mp-slls-snarlcut"
# vg mpmap --linear-index "${SLLS_INDEX}" \
# --linear-path "${GRAPH_CONTIG}" \
# -x "${GRAPHS_PATH}/snp1kg-${REGION_NAME}_filter.xg" \
# -g "${GRAPHS_PATH}/snp1kg-${REGION_NAME}_filter.gcsa" \
# --snarls "${GRAPHS_PATH}/snp1kg-${REGION_NAME}_filter.snarls" \
# --fastq "${READS_DIR}/sim.fq.gz" \
# -i \
# -S \
# -t 32 \
# >"${OUTPUT_PATH}/snp1kg-mp-slls-snarlcut/aligned-snp1kg-slls-snarlcut-pe_default.gam"
# fi
# # Then do the mapeval
# toil-vg mapeval "${TREE_PATH}/snp1kg-mp-slls-snarlcut" "${OUTPUT_PATH}/snp1kg-mp-slls-snarlcut" \
# --gams "${OUTPUT_PATH}/snp1kg-mp-slls-snarlcut/aligned-snp1kg-slls-snarlcut-pe_default.gam" \
# --config "${TREE_PATH}/toil-vg.conf" \
# --maxDisk 100G \
# --truth "${READS_DIR}/true.pos" \
# --index-bases "${GRAPHS_PATH}/snp1kg-${REGION_NAME}_filter" \
# --gam-names snp1kg-slls-snarlcut-mp-pe 2>&1 &
# JOB_ARRAY+=("$!")
#fi
#wait_on_jobs
fi
# Make all the jobs finish
MAX_JOBS=0
wait_on_jobs
if [[ ! -e "${OUTPUT_PATH}/position.results.tsv" ]]; then
# Concatenate all the conditions' position results files
FIRST_CONDITION=1
for CONDITION in "${CONDITIONS[@]}"; do
if [[ "${FIRST_CONDITION}" == "1" ]]; then
# Keep the header on the first condition we process
cat "${OUTPUT_PATH}/${CONDITION}/position.results.tsv" > "${OUTPUT_PATH}/position.results.tsv"
else
# Drop the header
cat "${OUTPUT_PATH}/${CONDITION}/position.results.tsv" | sed 1d >> "${OUTPUT_PATH}/position.results.tsv"
fi
FIRST_CONDITION=0
done
fi
if [[ ! -e "${OUTPUT_PATH}/qq" ]]; then
# Collect all the qq plots to one directory to page through easily
mkdir "${OUTPUT_PATH}/qq"
CONDITION_NUMBER=0
for CONDITION in "${CONDITIONS[@]}"; do
cp "${OUTPUT_PATH}/${CONDITION}/plot-qq.svg" "${OUTPUT_PATH}/qq/qq-${CONDITION_NUMBER}-${CONDITION}.svg"
((CONDITION_NUMBER+=1))
done
fi
if [[ ! -e "${OUTPUT_PATH}/table.tsv" ]]; then
# Make a table of wrong reads
# First we need a baseline for comparing against
BASELINE_CONDITION="snp1kg-mp-snarlcut"
# Make header for table of wrong read counts
printf "Condition\tWrong reads total\tAt MAPQ 60\tAt MAPQ 0\tAt MAPQ >0\tNew vs. ${BASELINE_CONDITION}\tFixed vs. ${BASELINE_CONDITION}\tAvg. Correct MAPQ\tCorrect MAPQ 0\n" > "${OUTPUT_PATH}/table.tsv"
# Pull out the baseline wrong reads
cat "${OUTPUT_PATH}/${BASELINE_CONDITION}/position.results.tsv" | sed 1d | grep -- "-pe" | grep -v "^1" | cut -f4 | sort > "${OUTPUT_PATH}/baseline-wrong-names.tsv"
for CONDITION in "${CONDITIONS[@]}"; do
# We want a table like
# Condition Wrong reads total At MAPQ 60 At MAPQ 0 At MAPQ >0 New vs. baseline Fixed vs. baseline
printf "${CONDITION}\t" >> "${OUTPUT_PATH}/table.tsv"
# Get the wrong reads for this condition
cat "${OUTPUT_PATH}/${CONDITION}/position.results.tsv" | sed 1d | grep -- "-pe" | grep -v "^1" > "${OUTPUT_PATH}/${CONDITION}/wrong.tsv"
# Wrong total
cat "${OUTPUT_PATH}/${CONDITION}/wrong.tsv" | wc -l | tr -d '\n' >> "${OUTPUT_PATH}/table.tsv"
printf "\t" >> "${OUTPUT_PATH}/table.tsv"
# Wrong at MAPQ 60
cat "${OUTPUT_PATH}/${CONDITION}/wrong.tsv" | grep -P "\t60\t" | wc -l | tr -d '\n' >> "${OUTPUT_PATH}/table.tsv"
printf "\t" >> "${OUTPUT_PATH}/table.tsv"
# Wrong at MAPQ 0
cat "${OUTPUT_PATH}/${CONDITION}/wrong.tsv" | grep -P "\t0\t" | wc -l | tr -d '\n' >> "${OUTPUT_PATH}/table.tsv"
printf "\t" >> "${OUTPUT_PATH}/table.tsv"
# Wrong at MAPQ >0
cat "${OUTPUT_PATH}/${CONDITION}/wrong.tsv" | grep -v -P "\t0\t" | wc -l | tr -d '\n' >> "${OUTPUT_PATH}/table.tsv"
printf "\t" >> "${OUTPUT_PATH}/table.tsv"
# Get the wrong read names for this condition
cat "${OUTPUT_PATH}/${CONDITION}/wrong.tsv" | cut -f4 | sort > "${OUTPUT_PATH}/${CONDITION}/wrong-names.tsv"
# Count newly wrong names (not in file 1 or both)
comm -1 -3 "${OUTPUT_PATH}/baseline-wrong-names.tsv" "${OUTPUT_PATH}/${CONDITION}/wrong-names.tsv" | wc -l | tr -d '\n' >> "${OUTPUT_PATH}/table.tsv"
printf "\t" >> "${OUTPUT_PATH}/table.tsv"
# Count newly right names (not in file 2 or both)
comm -2 -3 "${OUTPUT_PATH}/baseline-wrong-names.tsv" "${OUTPUT_PATH}/${CONDITION}/wrong-names.tsv" | wc -l | tr -d '\n' >> "${OUTPUT_PATH}/table.tsv"
printf "\t" >> "${OUTPUT_PATH}/table.tsv"
# Get the right reads
cat "${OUTPUT_PATH}/${CONDITION}/position.results.tsv" | sed 1d | grep -- "-pe" | grep "^1" > "${OUTPUT_PATH}/${CONDITION}/right.tsv"
# Compute average MAPQ for correct reads
# See <https://stackoverflow.com/a/19149931>
cat "${OUTPUT_PATH}/${CONDITION}/right.tsv" | cut -f2 | awk '{total += $1} END {if (NR > 0) {print total / NR} else {print "N/A"}}' | tr -d '\n' >> "${OUTPUT_PATH}/table.tsv"
printf "\t" >> "${OUTPUT_PATH}/table.tsv"
# Count correct reads at MAPQ 0
cat "${OUTPUT_PATH}/${CONDITION}/right.tsv" | grep -P "\t0\t" | wc -l | tr -d '\n' >> "${OUTPUT_PATH}/table.tsv"
printf "\n" >> "${OUTPUT_PATH}/table.tsv"
done
rm "${OUTPUT_PATH}/baseline-wrong-names.tsv"
fi
# Determine our source directory, where the ROC plotting script also lives
# See <https://stackoverflow.com/a/246128>
SCRIPT_DIRECTORY="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
# Do the R plots
if [[ ! -e "${OUTPUT_PATH}/roc.svg" ]]; then
Rscript "${SCRIPT_DIRECTORY}/plot-roc.R" "${OUTPUT_PATH}/position.results.tsv" "${OUTPUT_PATH}/roc.svg"
fi
if [[ ! -e "${OUTPUT_PATH}/pr.svg" ]]; then
Rscript "${SCRIPT_DIRECTORY}/plot-pr.R" "${OUTPUT_PATH}/position.results.tsv" "${OUTPUT_PATH}/pr.svg"
fi
rm "${TREE_PATH}/toil-vg.conf"
rmdir "${TREE_PATH}"
echo "Results available as plots ${OUTPUT_PATH}/roc.svg and ${OUTPUT_PATH}/pr.svg and table ${OUTPUT_PATH}/table.tsv"
|
