Release/1.0.0

CHANGELOG.md

@@ -1,5 +1,16 @@
 # Change Log
 
+## [1.0.0] - 2015-08-11
+### Added
+- Minimum ORF length filtering
+- Related options (Constant minimum length, percentage minimum length, adjustment for smaller read lengths)
+
+### Fixed
+- Translating edges of detected ORFs (previously were truncated)
+
+### Changed
+- A few minor description changes
+
 ## [0.2.1] - 2015-08-06
 ### Fixed
 - Alignment stats shown at completion now properly account for supplementary alignments

align.c

@@ -113,12 +113,12 @@ int command_align(int argc, char *argv[]) {
 
 	aux.opt = opt = mem_opt_init();
 	memset(&opt0, 0, sizeof(mem_opt_t));
-	opt->proteinFlag |= ALIGN_FLAG_BRUTEORF; // Temporary
 
-	while ((c = getopt(argc, argv, "1epabgnFMCSPVYju:k:o:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:h:y:K:X:H:")) >= 0) {
+	while ((c = getopt(argc, argv, "1epabgnMCSPVYJjf:F:u:k:o:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:h:y:K:X:H:")) >= 0) {
 		if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1;
 		else if (c == 'u') opt->outputType = atoi(optarg);
-		//else if (c == 'o') opt->min_orf_len = atoi(optarg);
+		else if (c == 'f') opt->min_orf_len = atoi(optarg);
+		else if (c == 'F') opt->min_orf_percent = atof(optarg);
 		else if (c == 'o') prefixName = optarg;
 		else if (c == '1') no_mt_io = 1;
 		else if (c == 'x') mode = optarg;
@@ -137,9 +137,10 @@ int command_align(int argc, char *argv[]) {
 		else if (c == 'F') opt->flag |= MEM_F_ALN_REG;
 		else if (c == 'Y') opt->flag |= MEM_F_SOFTCLIP;
 		else if (c == 'V') opt->flag |= MEM_F_REF_HDR;
-		else if (c == 'b') opt->proteinFlag &= ~ALIGN_FLAG_BRUTEORF;
+		else if (c == 'b') opt->proteinFlag &= ~ALIGN_FLAG_BRUTE_ORF;
 		else if (c == 'g') opt->proteinFlag |= ALIGN_FLAG_GEN_NT;
 		else if (c == 'n') opt->proteinFlag |= ALIGN_FLAG_KEEP_PRO;
+		else if (c == 'J') opt->proteinFlag &= ~ALIGN_FLAG_ADJUST_ORF;
 		else if (c == 'c') opt->max_occ = atoi(optarg), opt0.max_occ = 1;
 		else if (c == 'd') opt->zdrop = atoi(optarg), opt0.zdrop = 1;
 		else if (c == 'v') bwa_verbose = atoi(optarg);
@@ -389,9 +390,12 @@ int renderAlignUsage(const mem_opt_t * passOptions) {
 	fprintf(stderr, "\n");
 	fprintf(stderr, "Usage: paladin align [options] <idxbase> <in.fq>\n\n");
 
-	fprintf(stderr, "Protein detection options:\n\n");
+	fprintf(stderr, "Gene detection options:\n\n");
 	fprintf(stderr, "       -b            disable brute force ORF detection\n");
-	//fprintf(stderr, "       -l INT        minimum ORF length accepted during protein detection (DISABLED) [%d]\n", passOptions->min_orf_len);
+	fprintf(stderr, "       -J            do not adjust minimum ORF length (constant value) for shorter read lengths\n");
+	fprintf(stderr, "       -f INT        minimum ORF length accepted (as constant value) [%d]\n", passOptions->min_orf_len);
+	fprintf(stderr, "       -F FLOAT      minimum ORF length accepted (as percentage of read length) [%.2f]\n", passOptions->min_orf_percent);
+
 
 	fprintf(stderr, "\nAlignment options:\n\n");
 	fprintf(stderr, "       -t INT        number of threads [%d]\n", passOptions->n_threads);

bwamem.c

@@ -54,7 +54,6 @@ mem_opt_t *mem_opt_init()
 	o->outputStream = stdout;
 	o->outputType = OUTPUT_TYPE_UNIPROT_FULL;
 	o->flag = 0;
-	o->proteinFlag = 0;
 	o->a = 1; o->b = 1; //4;
 	o->o_del = o->o_ins = 6;
 	o->e_del = o->e_ins = 1;
@@ -63,10 +62,12 @@ mem_opt_t *mem_opt_init()
 	o->zdrop = 100;
 	o->pen_unpaired = 17;
 	o->pen_clip5 = o->pen_clip3 = 5;
-
 	o->max_mem_intv = 20;
-
-	o->min_orf_len = 180;
+	o->min_orf_len = 250;
+	o->min_orf_percent = 0;
+	o->proteinFlag = 0;
+	o->proteinFlag |= ALIGN_FLAG_BRUTE_ORF;
+	o->proteinFlag |= ALIGN_FLAG_ADJUST_ORF;
 	o->min_seed_len = 11;
 	o->split_width = 10;
 	o->max_occ = 500;

bwamem.h

@@ -44,7 +44,8 @@ typedef struct {
 	int flag;               // see MEM_F_* macros
 	int proteinFlag;		// see ALIGN_FLAG_* protein-related defines
 	int indexFlag;			// see INDEX_FLAG_* index/frame related defines
-	int min_orf_len;		// minimum ORF length accepted during protein detection
+	int min_orf_len;		// minimum ORF length accepted during protein detection (as constant value)
+	float min_orf_percent;	// minimum orf length accepted during protein detection (as percent of read length)
 	int min_seed_len;       // minimum seed length
 	int min_chain_weight;
 	int max_chain_extend;

main.c

@@ -1,6 +1,7 @@
 /*
    The MIT License
 
+   Copyright (c) 2015 by Anthony Westbrook, University of New Hampshire <[email protected]>
    Copyright (c) 2011 by Attractive Chaos <[email protected]>
 
    Permission is hereby granted, free of charge, to any person obtaining
@@ -22,27 +23,36 @@
    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.
+*/
 
-   Contact: Toni Westbrook <[email protected]>
-
+/*
    PALADIN (Protein Alignment and Detection Interface)
 
-   PALADIN is a protein sequence alignment tool based on the BWA source.  Like BWA, it aligns
-   sequences via read-mapping using BWT.  PALADIN, however, offers the novel approach
-   of aligning in the protein space.  During the index phase, it processes the reference genome's
-   nucleotide sequences and GTF/GFF annotation containing CDS entries, first
-   converting these transcripts into the corresponding protein sequences, then creating the BWT
-   and suffix array from these proteins.  During the alignment phase, it attempts to find ORFs in
-   the read sequences, then converts these to protein sequences, and aligns to the reference
-   protein sequences.
-
-   PALADIN currently only supports single-end reads, and BWA-MEM based alignment.  It makes
-   use of many BWA parameters and is therefore compatible with many of its command line arguments.
+   PALADIN is a protein sequence alignment tool designed for the accurate
+   functional characterization of metagenomes.
 
-   PALADIN IS CURRENTLY ALPHA AND HAS NOT BEEN FULLY TESTED.  USE AT YOUR OWN RISK.
-
-   For information regarding BWA, please contact its author, Heng Li <[email protected]>
+   PALADIN is based on BWA, and aligns sequences via read-mapping using
+   BWT. PALADIN, however, offers the novel approach of aligning in the
+   protein space. During the index phase, it processes the reference genome's
+   nucleotide sequences and GTF/GFF annotation containing CDS entries, first
+   converting these transcripts into the corresponding protein sequences, then
+   creating the BWT and suffix array from these proteins. The process of
+   translation is skiped when providing a protein reference file (e.g., UniProt)
+   for mapping. During the alignment phase, it attempts to find ORFs in the
+   read sequences, then converts these to protein sequences, and aligns to the
+   reference protein sequences.
+
+   PALADIN currently only supports single-end reads (or reads merged with FLASH,
+   PEAR, abyss-mergepairs), and BWA-MEM based alignment. It makes use of many
+   BWA parameters and is therefore compatible with many of its command line
+   arguments.
+
+   PALADIN may output a standard SAM file, or a text file containing a
+   UniProt-generated functional profile. This text file may be used for all
+   downstream characterizations.
 
+   Contact: Toni Westbrook <[email protected]>
+   For information regarding BWA, contact Heng Li <[email protected]>
 */
 
 #include <stdio.h>
@@ -130,5 +140,3 @@ int renderVersion() {
 
 	return 1;
 }
-
-

main.h

@@ -1,8 +1,66 @@
+/*
+   The MIT License
+
+   Copyright (c) 2015 by Anthony Westbrook, University of New Hampshire <[email protected]>
+   Copyright (c) 2011 by Attractive Chaos <[email protected]>
+
+   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.
+*/
+
+/*
+   PALADIN (Protein Alignment and Detection Interface)
+
+   PALADIN is a protein sequence alignment tool designed for the accurate
+   functional characterization of metagenomes.
+
+   PALADIN is based on BWA, and aligns sequences via read-mapping using
+   BWT. PALADIN, however, offers the novel approach of aligning in the
+   protein space. During the index phase, it processes the reference genome's
+   nucleotide sequences and GTF/GFF annotation containing CDS entries, first
+   converting these transcripts into the corresponding protein sequences, then
+   creating the BWT and suffix array from these proteins. The process of
+   translation is skiped when providing a protein reference file (e.g., UniProt)
+   for mapping. During the alignment phase, it attempts to find ORFs in the
+   read sequences, then converts these to protein sequences, and aligns to the
+   reference protein sequences.
+
+   PALADIN currently only supports single-end reads (or reads merged with FLASH,
+   PEAR, abyss-mergepairs), and BWA-MEM based alignment. It makes use of many
+   BWA parameters and is therefore compatible with many of its command line
+   arguments.
+
+   PALADIN may output a standard SAM file, or a text file containing a
+   UniProt-generated functional profile. This text file may be used for all
+   downstream characterizations.
+
+   Contact: Toni Westbrook <[email protected]>
+   For information regarding BWA, contact Heng Li <[email protected]>
+*/
+
+
 #ifndef MAIN_H_
 #define MAIN_H_
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.2.1"
+#define PACKAGE_VERSION "1.0.0"
 #endif
 
 // Render usage and version details