v1.8.1

LICENSE.md

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+The MIT License (MIT)
+
+Copyright (c) 2014 UFPR - Universidade Federal do Paraná (Vitor C. Piro - vitorpiro@gmail.com)
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

README.md

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+# FGAP: an automated gap closing tool 
+
+Piro, V. C., Faoro, H., Weiss, V. a, Steffens, M. B., Pedrosa, F. O., Souza, E. M., & Raittz, R. T. (2014). FGAP: an automated gap closing tool. BMC Research Notes, 7(1), 371. http://doi.org/10.1186/1756-0500-7-371
+
+Run (command line version with Octave):
+---------------------------------------
+
+	# On the same folder of the fgap.m script
+	octave --no-gui --eval 'fgap -d sample_data/DRAFT_ecoli_hiseq454.fasta -a sample_data/DATASET_ecoli_hiseq.fasta'
+
+Install and run (compiled version):
+-----------------------------------
+
+	# Download MCR
+	https://sourceforge.net/projects/fgap/files/MCR_LINUX64b.tar.gz
+
+	# Download compiled FGAP
+	https://sourceforge.net/projects/fgap/files/FGAP_1_8_1_LINUX64b.tar.gz
+
+	# Install MCR
+	tar xf MCR_LINUX64b.tar.gz
+	cd MCR_LINUX64b/
+	./installMCR.sh /home/user/MCR/
+
+	# Run FGAP
+	tar xf FGAP_1_8_1_LINUX64b.tar.gz
+	cd FGAP_1_8_1_LINUX64b/
+	./run_fgap.sh /home/user/MCR/v717/ -d sample_data/DRAFT_ecoli_hiseq454.fasta -a sample_data/DATASET_ecoli_hiseq.fasta
+
+Parameters:
+-----------
+
+	------------------------------------------
+					FGAP v1.8.1
+	------------------------------------------
+
+
+	Usage in command-line mode (compiled): ./run_fgap.sh <MCR installation folder> -d <draft file> -a "<dataset(s) file(s)>" [parameters]
+	Usage in Matlab/Octave (source): fgap -d <draft file> -a '<dataset(s) file(s)>' [parameters]
+
+	-d /--draft-file        Draft genome file [fasta format - Ex: 'draft.fasta']
+	-a /--datasets-files    List of datasets files to close gaps [fasta format - Ex: 'dataset1.fasta,dataset2.fasta']
+
+	-s /--min-score         Min Score (raw) to return results from BLAST (integer) - Default: 25
+	-e /--max-evalue        Max E-Value to return results from BLAST (float) - Default: 1e-7
+	-i /--min-identity      Min identity (%) to return results from BLAST (integer [0-100]) - Default: 70
+
+	-C /--contig-end-length Length (bp) of contig ends to perform BLAST alignment (integer) - Default: 300
+	-T /--edge-trim-length  Length of ignored bases (bp) upstream and downstrem of the gap (integer) - Default: 0
+	-R /--max-remove-length Max number of bases (bp) that can be removed (integer) - Default: 500
+	-I /--max-insert-length Max number of bases (bp) that can be inserted (integer) - Default: 500
+
+	-p /--positive-gap      Enable closing of positive gaps (with insertion) (integer [0-1]) - Default: 1
+	-z /--zero-gap          Enable closing of zero gaps (without insert any base) (integer [0-1]) - Default: 0
+	-g /--negative-gap      Enable closing of negative gaps (overlapping contig ends) (integer [0-1]) - Default: 0
+
+	-c /--gap-char                          Base that represents the gap (char) - Default: 'N'
+	-b /--blast-path                        Blast+ package path (only makeblastdb and blastn are needed, version 2.2.28+ or higher) - Default: ''
+	-l /--blast-alignment-parameters        BLAST alignment parameters (opengap,extendgap,match,mismatch,wordsize) - Default: '1,1,1,-3,15'
+	-r /--blast-max-results                 Max results from BLAST for each query (integer) - Default: 200
+	-t /--threads                           Number of threads (integer) - Default: 1
+
+	-m /--more-output       More output files with gap regions after and before gap closing (integer [0-1]) - Default: 0
+	-o /--output-prefix     Output prefix [File or folder - Ex: 'out' or 'out_folder/out' ] - Default: 'output_fgap'
+	-h /--help              This help message