<commit_before># Must already have a "built" version of the FASTA reference somewhere

TS=python $(TS_HOME)/bin/ts.py
TS_ARGS=--compress-output --verbose --write-all

r0_%.fq.mkb: r0_%.fq.gz
	$(MOSAIK_BUILD) -q $< -out $@ -st illumina

r12_%.fq.mkb: r1_%.fq.gz r2_%.fq.gz
	$(MOSAIK_BUILD) -q $< -q2 $(<:r1_%=r2_%) -out $@ -st illumina

define mosaikts

r0_$1_%.ts: r0_%.fq.mkb
	$$(TS) --ref $6 --mosaik-align-exe $$(MOSAIK_ALIGN) --mosaik-build-exe $$(MOSAIK_BUILD) --aligner=mosaik \
           --index $7 --sim-fraction 0.01 --sim-unp-min $2 $$(TS_ARGS) $4 --output-directory $$@ --U $$< \
           -- $5 $$(MOSAIK_ALIGN_ARGS) \
                 -annpe $(MOSAIK_HOME)/MOSAIK/networkFile/2.1.26.pe.100.0065.ann \
                 -annse $(MOSAIK_HOME)/MOSAIK/networkFile/2.1.26.se.100.005.ann
	-$$(MOSAIK_ALIGN) > $$@/mosaik_align_version 2>&1
	-$$(MOSAIK_BUILD) > $$@/mosaik_build_version 2>&1
	$$(TS) --version > $$@/ts_version

r12_$1_%.ts: r12_%.fq.mkb
	$$(TS) --ref $6 --bwa-exe $$(BWA) --aligner=bwa-mem  --index $7 --sim-fraction 0.01 \
	       --sim-conc-min $2 --sim-disc-min $3 --sim-bad-end-min $3 $$(TS_ARGS) $4 \<commit_msg>add extension for index<commit_after># Must already have a "built" version of the FASTA reference somewhere

TS=python $(TS_HOME)/bin/ts.py
TS_ARGS=--compress-output --verbose --write-all

r0_%.fq.mkb: r0_%.fq.gz
	$(MOSAIK_BUILD) -q $< -out $@ -st illumina

r12_%.fq.mkb: r1_%.fq.gz r2_%.fq.gz
	$(MOSAIK_BUILD) -q $< -q2 $(<:r1_%=r2_%) -out $@ -st illumina

define mosaikts

r0_$1_%.ts: r0_%.fq.mkb
	$$(TS) --ref $6 --mosaik-align-exe $$(MOSAIK_ALIGN) --mosaik-build-exe $$(MOSAIK_BUILD) --aligner=mosaik \
           --index $7.mosaik --sim-fraction 0.01 --sim-unp-min $2 $$(TS_ARGS) $4 --output-directory $$@ --U $$< \
           -- $5 $$(MOSAIK_ALIGN_ARGS) \
                 -annpe $(MOSAIK_HOME)/MOSAIK/networkFile/2.1.26.pe.100.0065.ann \
                 -annse $(MOSAIK_HOME)/MOSAIK/networkFile/2.1.26.se.100.005.ann
	-$$(MOSAIK_ALIGN) > $$@/mosaik_align_version 2>&1
	-$$(MOSAIK_BUILD) > $$@/mosaik_build_version 2>&1
	$$(TS) --version > $$@/ts_version

r12_$1_%.ts: r12_%.fq.mkb
	$$(TS) --ref $6 --bwa-exe $$(BWA) --aligner=bwa-mem  --index $7.mosaik --sim-fraction 0.01 \
	       --sim-conc-min $2 --sim-disc-min $3 --sim-bad-end-min $3 $$(TS_ARGS) $4 \
{'fraction_non_alphanumeric': 0.2230902777777778, 'fraction_numerical': 0.051215277777777776, 'mean_word_length': 2.717741935483871, 'pattern_counts': {'":': 0, '<': 11, '<?xml version=': 0, '>': 13, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4603899', 'n_tokens_mistral': 1134, 'n_tokens_neox': 1056, 'n_words': 185}