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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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data/cds/sp_chlorodb/parameters.sh Normal file
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# sourced file
set CORE_NCDS_CUTOFF = 200
set CORE_START_ATG_CUTOFF = 50
set CORE_START_DFT_CUTOFF = 50
set CORE_START_OTH_CUTOFF = 10
set CORE_STOP_CUTOFF = 200
set CORE_SPLICE_CUTOFF = 50
set SHEL_NCDS_CUTOFF = 10
set CORE_DELTA = Inf
set CORE_COVMIN = 30
set CORE_PMAX = 1e-6
set CORE_IDMIN = 30
set CORE_SIZMIN = 50
set SHEL_DELTA = 0.5
set SHEL_COVMIN = 30
set SHEL_PMAX = 1e-6
set SHEL_IDMIN = 30
set SHEL_SIZMIN = 10
set DUST_DELTA = 0.5
set DUST_COVMIN = 30
set DUST_PMAX = 1e-6
set DUST_IDMIN = 30
set DUST_SIZMIN = 10

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