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A bit stronger filtering for mappings and matches #351

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Nov 3, 2023
Merged

A bit stronger filtering for mappings and matches #351

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58ed548
a bit stronger filtering for mappings and matches
AndreaGuarracino Nov 3, 2023
2da7b7d
tweak
AndreaGuarracino Nov 3, 2023
8ffba9b
typo
AndreaGuarracino Nov 3, 2023
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12 changes: 9 additions & 3 deletions partition-before-pggb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@ SEGMENT_LENGTH=5000
MAP_PCT_ID=90
MASH_KMER=19
MASH_KMER_THRES=0.001
HG_FILTER_ANI_DIFF=30

# wfmash's parameters
input_fasta=false
Expand All @@ -20,10 +21,11 @@ no_splits=false
sparse_map=false
mash_kmer=$MASH_KMER
mash_kmer_thres=$MASH_KMER_THRES
hg_filter_ani_diff=$HG_FILTER_ANI_DIFF
exclude_delim="#"

# seqwish's default values
MIN_MATCH_LENGTH=19
MIN_MATCH_LENGTH=23
SPARSE_FACTOR=0
TRANSCLOSE_BATCH=10000000

Expand Down Expand Up @@ -116,7 +118,7 @@ fi

# read the options
cmd=$0" "$@
TEMP=`getopt -o i:o:D:a:p:c:s:l:K:F:k:x:f:B:Xn:j:P:O:Me:t:T:vhASY:G:Q:d:I:R:NbrmZzV: --long input-fasta:,output-dir:,temp-dir:,input-paf:,map-pct-id:,n-mappings:,segment-length:,block-length-min:,mash-kmer:,mash-kmer-thres:,min-match-length:,sparse-map:,sparse-factor:,transclose-batch:,skip-normalization,n-haplotypes:,path-jump-max:,subpath-min:,edge-jump-max:,threads:,poa-threads:,skip-viz,do-layout,help,no-merge-segments,stats,exclude-delim:,poa-length-target:,poa-params:,poa-padding:,run-abpoa,global-poa,write-maf,consensus-spec:,consensus-prefix:,pad-max-depth:,block-id-min:,block-ratio-min:,no-splits,resume,keep-temp-files,multiqc,compress,vcf-spec:,version -n 'pggb' -- "$@"`
TEMP=`getopt -o i:o:D:a:p:c:g:s:l:K:F:k:x:f:B:Xn:j:P:O:Me:t:T:vhASY:G:Q:d:I:R:NbrmZzV: --long input-fasta:,output-dir:,temp-dir:,input-paf:,map-pct-id:,n-mappings:,hg-filter-ani-diff:,segment-length:,block-length-min:,mash-kmer:,mash-kmer-thres:,min-match-length:,sparse-map:,sparse-factor:,transclose-batch:,skip-normalization,n-haplotypes:,path-jump-max:,subpath-min:,edge-jump-max:,threads:,poa-threads:,skip-viz,do-layout,help,no-merge-segments,stats,exclude-delim:,poa-length-target:,poa-params:,poa-padding:,run-abpoa,global-poa,write-maf,consensus-spec:,consensus-prefix:,pad-max-depth:,block-id-min:,block-ratio-min:,no-splits,resume,keep-temp-files,multiqc,compress,vcf-spec:,version -n 'pggb' -- "$@"`
eval set -- "$TEMP"

# extract options and their arguments into variables.
Expand All @@ -127,6 +129,7 @@ while true ; do
-l|--block-length) block_length=$(parse_numeric $2) ; shift 2 ;;
-p|--map-pct-id) map_pct_id=$2 ; shift 2 ;;
-c|--n-mappings) n_mappings=$2 ; shift 2 ;;
-g|--hg-filter-ani-diff) hg_filter_ani_diff=$2 ; shift 2 ;;
-N|--no-splits) no_splits=true ; shift ;;
-x|--sparse-map) sparse_map=$2 ; shift 2 ;;
-K|--mash-kmer) mash_kmer=$2 ; shift 2 ;;
Expand Down Expand Up @@ -187,6 +190,7 @@ if [ "$show_help" == true ]; then
echo " -l, --block-length N minimum block length filter for mapping [default: 5*segment-length]"
echo " -p, --map-pct-id PCT percent identity for mapping/alignment [default: "$MAP_PCT_ID"]"
echo " -c, --n-mappings N number of mappings for each segment [default: 1]"
echo " -g, --hg-filter-ani-diff N filter out mappings unlikely to be N% less than the best mapping [default: "$HG_FILTER_ANI_DIFF"%]"
echo " -N, --no-split disable splitting of input sequences during mapping [default: enabled]"
echo " -x, --sparse-map N keep this fraction of mappings ('auto' for giant component heuristic) [default: 1.0]"
echo " -K, --mash-kmer N kmer size for mapping [default: "$MASH_KMER"]"
Expand Down Expand Up @@ -303,7 +307,7 @@ if [[ $block_length == false ]]; then
fi


paf_spec=$mapper_letter-s$segment_length-l$block_length-p$map_pct_id-n$n_mappings-K$mash_kmer-F$mash_kmer_thres-x$sparse_map
paf_spec=$mapper_letter-s$segment_length-l$block_length-p$map_pct_id-n$n_mappings-K$mash_kmer-F$mash_kmer_thres-x$sparse_map-g$hg_filter_ani_diff

split_cmd=""
if [[ $no_splits == true ]]; then
Expand Down Expand Up @@ -437,6 +441,7 @@ $mapper:
sparse-map: $sparse_map
mash-kmer: $mash_kmer
mash-kmer-thres: $mash_kmer_thres
hg-filter-ani-diff: $hg_filter_ani_diff
exclude-delim: $exclude_delim
no-merge-segments: $no_merge_segments
seqwish:
Expand Down Expand Up @@ -496,6 +501,7 @@ if [[ "$input_paf" == false ]]; then
$merge_cmd \
"$input_fasta" \
--lower-triangular \
--hg-filter-ani-diff $hg_filter_ani_diff \
--approx-map \
> "$prefix_mappings_paf".mappings.$mapper.paf) 2> >(tee -a "$log_file")
fi
Expand Down
13 changes: 10 additions & 3 deletions pggb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@ SEGMENT_LENGTH=5000
MAP_PCT_ID=90
MASH_KMER=19
MASH_KMER_THRES=0.001
HG_FILTER_ANI_DIFF=30

# wfmash's parameters
input_fasta=false
Expand All @@ -20,10 +21,11 @@ no_splits=false
sparse_map=false
mash_kmer=$MASH_KMER
mash_kmer_thres=$MASH_KMER_THRES
hg_filter_ani_diff=$HG_FILTER_ANI_DIFF
exclude_delim="#"

# seqwish's default values
MIN_MATCH_LENGTH=19
MIN_MATCH_LENGTH=23
SPARSE_FACTOR=0
TRANSCLOSE_BATCH=10000000

Expand Down Expand Up @@ -116,7 +118,7 @@ fi

# read the options
cmd=$0" "$@
TEMP=`getopt -o i:o:D:a:p:c:s:l:K:F:k:x:f:B:Xn:j:P:O:Me:t:T:vhASY:G:Q:d:I:R:NbrmZzV: --long input-fasta:,output-dir:,temp-dir:,input-paf:,map-pct-id:,n-mappings:,segment-length:,block-length-min:,mash-kmer:,mash-kmer-thres:,min-match-length:,sparse-map:,sparse-factor:,transclose-batch:,skip-normalization,n-haplotypes:,path-jump-max:,subpath-min:,edge-jump-max:,threads:,poa-threads:,skip-viz,do-layout,help,no-merge-segments,stats,exclude-delim:,poa-length-target:,poa-params:,poa-padding:,run-abpoa,global-poa,write-maf,consensus-spec:,consensus-prefix:,pad-max-depth:,block-id-min:,block-ratio-min:,no-splits,resume,keep-temp-files,multiqc,compress,vcf-spec:,version -n 'pggb' -- "$@"`
TEMP=`getopt -o i:o:D:a:p:c:g:s:l:K:F:k:x:f:B:Xn:j:P:O:Me:t:T:vhASY:G:Q:d:I:R:NbrmZzV: --long input-fasta:,output-dir:,temp-dir:,input-paf:,map-pct-id:,n-mappings:,hg-filter-ani-diff:,segment-length:,block-length-min:,mash-kmer:,mash-kmer-thres:,min-match-length:,sparse-map:,sparse-factor:,transclose-batch:,skip-normalization,n-haplotypes:,path-jump-max:,subpath-min:,edge-jump-max:,threads:,poa-threads:,skip-viz,do-layout,help,no-merge-segments,stats,exclude-delim:,poa-length-target:,poa-params:,poa-padding:,run-abpoa,global-poa,write-maf,consensus-spec:,consensus-prefix:,pad-max-depth:,block-id-min:,block-ratio-min:,no-splits,resume,keep-temp-files,multiqc,compress,vcf-spec:,version -n 'pggb' -- "$@"`
eval set -- "$TEMP"

# extract options and their arguments into variables.
Expand All @@ -127,6 +129,7 @@ while true ; do
-l|--block-length) block_length=$(parse_numeric $2) ; shift 2 ;;
-p|--map-pct-id) map_pct_id=$2 ; shift 2 ;;
-c|--n-mappings) n_mappings=$2 ; shift 2 ;;
-g|--hg-filter-ani-diff) hg_filter_ani_diff=$2 ; shift 2 ;;
-N|--no-splits) no_splits=true ; shift ;;
-x|--sparse-map) sparse_map=$2 ; shift 2 ;;
-K|--mash-kmer) mash_kmer=$2 ; shift 2 ;;
Expand Down Expand Up @@ -187,6 +190,7 @@ if [ "$show_help" == true ]; then
echo " -l, --block-length N minimum block length filter for mapping [default: 5*segment-length]"
echo " -p, --map-pct-id PCT percent identity for mapping/alignment [default: "$MAP_PCT_ID"]"
echo " -c, --n-mappings N number of mappings for each segment [default: 1]"
echo " -g, --hg-filter-ani-diff N filter out mappings unlikely to be N% less than the best mapping [default: "$HG_FILTER_ANI_DIFF"%]"
echo " -N, --no-split disable splitting of input sequences during mapping [default: enabled]"
echo " -x, --sparse-map N keep this fraction of mappings ('auto' for giant component heuristic) [default: 1.0]"
echo " -K, --mash-kmer N kmer size for mapping [default: "$MASH_KMER"]"
Expand Down Expand Up @@ -303,7 +307,7 @@ if [[ $block_length == false ]]; then
fi


paf_spec=$mapper_letter-s$segment_length-l$block_length-p$map_pct_id-n$n_mappings-K$mash_kmer-F$mash_kmer_thres-x$sparse_map
paf_spec=$mapper_letter-s$segment_length-l$block_length-p$map_pct_id-n$n_mappings-K$mash_kmer-F$mash_kmer_thres-x$sparse_map-g$hg_filter_ani_diff

split_cmd=""
if [[ $no_splits == true ]]; then
Expand Down Expand Up @@ -437,6 +441,7 @@ $mapper:
sparse-map: $sparse_map
mash-kmer: $mash_kmer
mash-kmer-thres: $mash_kmer_thres
hg-filter-ani-diff: $hg_filter_ani_diff
exclude-delim: $exclude_delim
no-merge-segments: $no_merge_segments
seqwish:
Expand Down Expand Up @@ -500,6 +505,7 @@ if [[ "$input_paf" == false ]]; then
$merge_cmd \
"$input_fasta" \
--lower-triangular \
--hg-filter-ani-diff $hg_filter_ani_diff \
--approx-map \
> "$prefix_mappings_paf".mappings.$mapper.paf) 2> >(tee -a "$log_file")
fi
Expand All @@ -519,6 +525,7 @@ if [[ "$input_paf" == false ]]; then
$merge_cmd \
"$input_fasta" \
--lower-triangular \
--hg-filter-ani-diff $hg_filter_ani_diff \
-i "$prefix_mappings_paf".mappings.$mapper.paf --invert-filtering \
> "$prefix_paf".alignments.$mapper.paf) 2> >(tee -a "$log_file")
fi
Expand Down
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