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modified:   .gitignore
	new file:   data/cds/sp_chlorodb/parameters.sh
	deleted:    data/ir/LSC_RefDB.fasta
	deleted:    data/ir/SSC_RefDB.fasta
	modified:   detectors/cds/bin/go_cds.sh
	modified:   detectors/normalize/lib/lookforIR.lib.sh
	modified:   detectors/normalize/lib/selectIR.py
	modified:   organnot/Dockerfile
	new file:   organnot/README.md
	new file:   organnot/dorgannot
	deleted:    ports/.DS_Store
	deleted:    src/ncbiblast/binaries/.gitignore
	deleted:    src/prokov/lxpack/tests/S.fasta
	deleted:    src/prokov/lxpack/tests/St.fasta
	deleted:    src/prokov/lxpack/tests/Stt.fasta
	deleted:    src/prokov/lxpack/tests/aS.fasta
	deleted:    src/prokov/lxpack/tests/aSt.fasta
	deleted:    src/prokov/lxpack/tests/aStt.fasta
	deleted:    src/prokov/lxpack/tests/aaS.fasta
	deleted:    src/prokov/lxpack/tests/aaSt.fasta
	deleted:    src/prokov/lxpack/tests/aaStt.fasta
	new file:   src/repseek/repseek-2014.09.tgz
This commit is contained in:
Eric Coissac
2025-03-05 21:56:39 +01:00
parent 5d09615f27
commit 4b71fe8c4c
22 changed files with 94 additions and 75646 deletions
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6
detectors/normalize/lib/lookforIR.lib.sh
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@ -27,9 +27,9 @@ function lookForIR {
-outfmt 6 \
-max_target_seqs 10000 | \
awk -v id_match=80 -v lmin=100 \
'($4 > lmin) && (($3+0)>id_match) {
SAME=(($7 < $8) && ($9 < $10)) || (($7 > $8) && ($9 > $10));
if ($7 < $8)
'($4+0 > lmin) && (($3+0)>id_match) {
SAME=(($7+0 < $8+0) && ($9+0 < $10+0)) || (($7+0 > $8+0) && ($9+0 > $10+0));
if ($7+0 < $8+0)
{print substr($2,1,3),$7,$8,SAME}
else
{print substr($2,1,3),$8,$7,SAME}