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Output getdamage stats as a gzip file #40

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Merged
fgvieira merged 1 commit into from
Jun 30, 2025
Merged

Output getdamage stats as a gzip file #40

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15 changes: 7 additions & 8 deletions metaDMG.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -311,24 +311,23 @@ int main_getdamage(int argc, char **argv) {

// write stat
char buf[1024];
snprintf(buf, 1024, "%s.stat", onam);
snprintf(buf, 1024, "%s.stat.gz", onam);
fprintf(stderr, "\t-> Outputting overall statistic in file: \"%s\"\n", buf);

FILE *fpstat = NULL;
assert(((fpstat = fopen(buf, "wb"))) != NULL);
fprintf(fpstat,"taxid\tnreads\tmea_len\tvar_len\tmean_gc\tvar_gc\tlca\trank\n");
gzFile fpstat = NULL;
assert((fpstat = gzopen(buf, "wb")) != NULL);
gzprintf(fpstat,"taxid\tnreads\tmea_len\tvar_len\tmean_gc\tvar_gc\tlca\trank\n");
for (std::map<int, std::vector<float> >::iterator it = gcconts.begin(); it != gcconts.end(); it++) {
std::map<int, triple>::iterator it2 = dmg->assoc.find(it->first);
assert(it2 != dmg->assoc.end());
std::map<int, std::vector<float> >::iterator it3 = seqlens.find(it->first);
assert(it3 != seqlens.end());
if (0)
fprintf(fpstat, "%d\t%lu\t%f\t%f\t%f\t%f\tNA\tNA\n", it->first, it2->second.nreads, mean(it3->second), var(it3->second), mean(it->second), var(it->second));
gzprintf(fpstat, "%d\t%lu\t%f\t%f\t%f\t%f\tNA\tNA\n", it->first, it2->second.nreads, mean(it3->second), var(it3->second), mean(it->second), var(it->second));
else
fprintf(fpstat, "%s\t%lu\t%f\t%f\t%f\t%f\tNA\tNA\n", sam_hdr_tid2name(hdr, it->first), it2->second.nreads, mean(it3->second), var(it3->second), mean(it->second), var(it->second));
gzprintf(fpstat, "%s\t%lu\t%f\t%f\t%f\t%f\tNA\tNA\n", sam_hdr_tid2name(hdr, it->first), it2->second.nreads, mean(it3->second), var(it3->second), mean(it->second), var(it->second));
}
if (fpstat != NULL)
fclose(fpstat);
gzclose(fpstat);

sam_hdr_destroy(hdr);
bam_destroy1(b);
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8 changes: 4 additions & 4 deletions test/testAll.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,7 @@ if [[ $? -ne 0 ]]; then
echo "Problem running command: ${CMD}"
RVAL=$((32+RVAL))
fi
gunzip -c output/test_lca.lca.gz |cut -f1,3-100 >output/test_lca.lca.sub
gunzip -c output/test_lca.lca.gz | cut -f1,3-100 >output/test_lca.lca.sub

echo "Running aggregate"
CMD="${PRG} aggregate output/test_lca.bdamage.gz --nodes data/nodes.dmp.gz --names data/names.dmp.gz --lcastat output/test_lca.stat.gz --out_prefix output/test_aggregate"
Expand All @@ -87,13 +87,13 @@ fi
echo "Running test of output/test_dfit_local.dfit.gz by gzip -t output/test_dfit_local.dfit.gz "
gzip -t output/test_dfit_local.dfit.gz
echo -ne "Return value of test $?\nWill now run gunzip -c output/test_dfit_local.dfit.gz|wc -c\n"
gunzip -c output/test_dfit_local.dfit.gz|wc -c
gunzip -c output/test_dfit_local.dfit.gz | wc -c


gunzip -c output/test_dfit_local.dfit.gz > tmp.txt
head -n 10 tmp.txt > tmp2.txt
#rm tmp.txt
cut -f 1-6,8- tmp2.txt| numfmt -d $'\t' --header --format='%.2f' --field=2- --invalid=ignore > output/test_dfit_local.dfit.fix
cut -f 1-6,8- tmp2.txt | numfmt -d $'\t' --header --format='%.2f' --field=2- --invalid=ignore > output/test_dfit_local.dfit.fix
#rm tmp2.txt
#zcat output/test_dfit_local.dfit.gz | head -n 10|cut -f 1-6,8- | numfmt -d $'\t' --header --format='%.2f' --field=2- --invalid=ignore > output/test_dfit_local.dfit.fix
#exit 0
Expand All @@ -112,7 +112,7 @@ fi
gunzip -c output/test_dfit_local_10threads.dfit.gz > tmp.txt
head -n 10 tmp.txt > tmp2.txt
rm tmp.txt
cut -f 1-6,8- tmp2.txt| numfmt -d $'\t' --header --format='%.2f' --field=2- --invalid=ignore | sort -r > output/test_dfit_local_10threads.dfit.fix
cut -f 1-6,8- tmp2.txt | numfmt -d $'\t' --header --format='%.2f' --field=2- --invalid=ignore | sort -r > output/test_dfit_local_10threads.dfit.fix
rm tmp2.txt

echo "Running dfit global"
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