| | |
| | |
| | |
| | |
| |
|
| | fstaln ?= ${WDIR}/crp/trn/aln/fast |
| | fstaln.in = $(addprefix ${WDIR}/crp/trn/pll/clean/, ${pllshards}) |
| | |
| | symal_grow_diag_final_and = -a=g -d=yes -f=yes -b=yes |
| | symal_args = ${symal_grow_diag_final_and} |
| |
|
| | fastalign: | pll-ready |
| | fastalign: options = -d -v -o |
| | fastalign: $(fstaln)/${L1}.txt.gz |
| | fastalign: $(fstaln)/${L2}.txt.gz |
| | fastalign: $(fstaln)/${L1}-${L2}.symal.gz |
| |
|
| | .INTERMEDIATE: $(fstaln)/tmp/${L1}-${L2}.fwd.gz |
| | .INTERMEDIATE: $(fstaln)/tmp/${L1}-${L2}.bwd.gz |
| | $(fstaln)/${L1}-${L2}.symal.gz: | $(fstaln)/tmp/${L1}-${L2}.fwd.gz |
| | $(fstaln)/${L1}-${L2}.symal.gz: | $(fstaln)/tmp/${L1}-${L2}.bwd.gz |
| | $(fstaln)/${L1}-${L2}.symal.gz: | $(fstaln)/${L1}.txt.gz |
| | $(fstaln)/${L1}-${L2}.symal.gz: | $(fstaln)/${L2}.txt.gz |
| | $(lock) |
| | ${m4mdir}/scripts/fast-align2bal.py \ |
| | <(zcat $(fstaln)/${L1}.txt.gz) \ |
| | <(zcat $(fstaln)/${L2}.txt.gz) \ |
| | <(zcat $(fstaln)/tmp/${L1}-${L2}.fwd.gz) \ |
| | <(zcat $(fstaln)/tmp/${L1}-${L2}.bwd.gz) \ |
| | | ${symal} ${symal_args} | gzip > $@_ && mv $@_ $@ |
| | rm -rf $(fstaln)/tmp |
| | $(unlock) |
| |
|
| | .INTERMEDIATE: $(fstaln)/tmp/${L1}-${L2}.txt |
| | $(fstaln)/tmp/${L1}-${L2}.txt: | $(fstaln)/${L1}.txt.gz |
| | $(fstaln)/tmp/${L1}-${L2}.txt: | $(fstaln)/${L2}.txt.gz |
| | $(lock) |
| | paste -d '\t' <(zcat $(fstaln)/${L1}.txt.gz) <(zcat $(fstaln)/${L2}.txt.gz) \ |
| | | perl -pe 's/\t/ \|\|\| /' > $@_ && mv $@_ $@ |
| | $(unlock) |
| |
|
| | $(fstaln)/tmp/${L1}-${L2}.fwd.gz: options ?= |
| | $(fstaln)/tmp/${L1}-${L2}.fwd.gz: | $(fast_align) |
| | $(fstaln)/tmp/${L1}-${L2}.fwd.gz: | $(fstaln)/tmp/${L1}-${L2}.txt |
| | $(fstaln)/tmp/${L1}-${L2}.fwd.gz: |
| | $(lock) |
| | ${fast_align} -i ${@D}/${L1}-${L2}.txt ${options} | gzip > $@_ && mv $@_ $@ |
| | $(unlock) |
| |
|
| | $(fstaln)/tmp/${L1}-${L2}.bwd.gz: options ?= |
| | $(fstaln)/tmp/${L1}-${L2}.bwd.gz: | $(fast_align) |
| | $(fstaln)/tmp/${L1}-${L2}.bwd.gz: | $(fstaln)/tmp/${L1}-${L2}.txt |
| | $(fstaln)/tmp/${L1}-${L2}.bwd.gz: |
| | $(lock) |
| | ${fast_align} -r -i ${@D}/${L1}-${L2}.txt ${options} | gzip > $@_ && mv $@_ $@ |
| | $(unlock) |
| |
|
| | $(fstaln)/${L2}.txt.gz: | $(addsuffix .${L2}.gz, ${fstaln.in}) |
| | $(lock) |
| | ifeq ($(words ${pllshards}),1) |
| | @cp -l $| $@ || cp $| $@ |
| | else |
| | @cat $| > $@_ && mv $@_ $@ |
| | endif |
| | $(unlock) |
| |
|
| | $(fstaln)/${L1}.txt.gz: | $(addsuffix .${L1}.gz, ${fstaln.in}) |
| | $(lock) |
| | ifeq ($(words ${pllshards}),1) |
| | @cp -l $| $@ || cp $| $@ |
| | else |
| | @cat $| > $@_ && mv $@_ $@ |
| | endif |
| | $(unlock) |
| |
|
| | |
| | fast-align.git = https://github.com/clab/fast_align.git |
| | ${fast_align}: |
| | $(lock) |
| | git clone ${fast-align.git} |
| | cd fast_align && make |
| | mkdir -p $(dir ${fast_align}) |
| | cp fast_align/fast_align $(dir ${fast_align}) |
| | rm -rf fast_align |
| | $(unlock) |
| |
|