r671: cleanup command line options

Author: lh3

main.c

@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "getopt.h"
 
-#define MM_VERSION "2.7-r670-dirty"
+#define MM_VERSION "2.7-r671-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>
@@ -28,7 +28,7 @@ static struct option long_options[] = {
 	{ "seed",           required_argument, 0, 0 },
 	{ "no-kalloc",      no_argument,       0, 0 },
 	{ "print-qname",    no_argument,       0, 0 },
-	{ "no-self",        no_argument,       0, 0 },
+	{ "no-self",        no_argument,       0, 'D' },
 	{ "print-seeds",    no_argument,       0, 0 },
 	{ "max-chain-skip", required_argument, 0, 0 },
 	{ "min-dp-len",     required_argument, 0, 0 },
@@ -37,17 +37,19 @@ static struct option long_options[] = {
 	{ "cost-non-gt-ag", required_argument, 0, 'C' },
 	{ "no-long-join",   no_argument,       0, 0 },
 	{ "sr",             no_argument,       0, 0 },
-	{ "frag",           optional_argument, 0, 0 },
-	{ "secondary",      optional_argument, 0, 0 },
+	{ "frag",           required_argument, 0, 0 },
+	{ "secondary",      required_argument, 0, 0 },
 	{ "cs",             optional_argument, 0, 0 },
 	{ "end-bonus",      required_argument, 0, 0 },
 	{ "no-pairing",     no_argument,       0, 0 },
-	{ "splice-flank",   optional_argument, 0, 0 },
+	{ "splice-flank",   required_argument, 0, 0 },
 	{ "idx-no-seq",     no_argument,       0, 0 },
 	{ "end-seed-pen",   required_argument, 0, 0 },   // 21
 	{ "for-only",       no_argument,       0, 0 },   // 22
 	{ "rev-only",       no_argument,       0, 0 },   // 23
-	{ "heap-sort",      optional_argument, 0, 0 },   // 24
+	{ "heap-sort",      required_argument, 0, 0 },   // 24
+	{ "all-chain",      no_argument,       0, 'P' },
+	{ "dual",           required_argument, 0, 0 },   // 26
 	{ "help",           no_argument,       0, 'h' },
 	{ "max-intron-len", required_argument, 0, 'G' },
 	{ "version",        no_argument,       0, 'V' },
@@ -70,9 +72,22 @@ static inline int64_t mm_parse_num(const char *str)
 	return (int64_t)(x + .499);
 }
 
+static inline void yes_or_no(mm_mapopt_t *opt, int flag, int long_idx, const char *arg, int yes_to_set)
+{
+	if (yes_to_set) {
+		if (strcmp(arg, "yes") == 0 || strcmp(arg, "y") == 0) opt->flag |= flag;
+		else if (strcmp(arg, "no") == 0 || strcmp(arg, "n") == 0) opt->flag &= ~flag;
+		else fprintf(stderr, "[WARNING]\033[1;31m option '--%s' only accepts 'yes' or 'no'.\033[0m\n", long_options[long_idx].name);
+	} else {
+		if (strcmp(arg, "yes") == 0 || strcmp(arg, "y") == 0) opt->flag &= ~flag;
+		else if (strcmp(arg, "no") == 0 || strcmp(arg, "n") == 0) opt->flag |= flag;
+		else fprintf(stderr, "[WARNING]\033[1;31m option '--%s' only accepts 'yes' or 'no'.\033[0m\n", long_options[long_idx].name);
+	}
+}
+
 int main(int argc, char *argv[])
 {
-	const char *opt_str = "2aSw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:R:hF:LC:";
+	const char *opt_str = "2aSDw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:R:hF:LC:";
 	mm_mapopt_t opt;
 	mm_idxopt_t ipt;
 	int i, c, n_threads = 3, long_idx;
@@ -111,7 +126,9 @@ int main(int argc, char *argv[])
 		else if (c == 'p') opt.pri_ratio = atof(optarg);
 		else if (c == 'M') opt.mask_level = atof(optarg);
 		else if (c == 'c') opt.flag |= MM_F_OUT_CG | MM_F_CIGAR;
-		else if (c == 'X') opt.flag |= MM_F_AVA | MM_F_NO_SELF;
+		else if (c == 'D') opt.flag |= MM_F_NO_DIAG;
+		else if (c == 'P') opt.flag |= MM_F_ALL_CHAINS;
+		else if (c == 'X') opt.flag |= MM_F_ALL_CHAINS | MM_F_NO_DIAG | MM_F_NO_DUAL | MM_F_NO_LJOIN; // -D -P --no-long-join --dual=no
 		else if (c == 'a') opt.flag |= MM_F_OUT_SAM | MM_F_CIGAR;
 		else if (c == 'Q') opt.flag |= MM_F_NO_QUAL;
 		else if (c == 'Y') opt.flag |= MM_F_SOFTCLIP;
@@ -133,7 +150,6 @@ int main(int argc, char *argv[])
 		else if (c == 0 && long_idx == 2) opt.seed = atoi(optarg); // --seed
 		else if (c == 0 && long_idx == 3) mm_dbg_flag |= MM_DBG_NO_KALLOC; // --no-kalloc
 		else if (c == 0 && long_idx == 4) mm_dbg_flag |= MM_DBG_PRINT_QNAME; // --print-qname
-		else if (c == 0 && long_idx == 5) opt.flag |= MM_F_NO_SELF; // --no-self
 		else if (c == 0 && long_idx == 6) mm_dbg_flag |= MM_DBG_PRINT_QNAME | MM_DBG_PRINT_SEED, n_threads = 1; // --print-seed
 		else if (c == 0 && long_idx == 7) opt.max_chain_skip = atoi(optarg); // --max-chain-skip
 		else if (c == 0 && long_idx == 8) opt.min_ksw_len = atoi(optarg); // --min-dp-len
@@ -148,13 +164,9 @@ int main(int argc, char *argv[])
 		else if (c == 0 && long_idx ==22) opt.flag |= MM_F_FOR_ONLY; // --for-only
 		else if (c == 0 && long_idx ==23) opt.flag |= MM_F_REV_ONLY; // --rev-only
 		else if (c == 0 && long_idx == 14) { // --frag
-			if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
-				opt.flag |= MM_F_FRAG_MODE;
-			else opt.flag &= ~MM_F_FRAG_MODE;
+			yes_or_no(&opt, MM_F_FRAG_MODE, long_idx, optarg, 1);
 		} else if (c == 0 && long_idx == 15) { // --secondary
-			if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
-				opt.flag &= ~MM_F_NO_PRINT_2ND;
-			else opt.flag |= MM_F_NO_PRINT_2ND;
+			yes_or_no(&opt, MM_F_NO_PRINT_2ND, long_idx, optarg, 0);
 		} else if (c == 0 && long_idx == 16) { // --cs
 			opt.flag |= MM_F_OUT_CS | MM_F_CIGAR;
 			if (optarg == 0 || strcmp(optarg, "short") == 0) {
@@ -167,13 +179,11 @@ int main(int argc, char *argv[])
 				fprintf(stderr, "[WARNING]\033[1;31m --cs only takes 'short' or 'long'. Invalid values are assumed to be 'short'.\033[0m\n");
 			}
 		} else if (c == 0 && long_idx == 19) { // --splice-flank
-			if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
-				opt.flag |= MM_F_SPLICE_FLANK;
-			else opt.flag &= ~MM_F_SPLICE_FLANK;
+			yes_or_no(&opt, MM_F_SPLICE_FLANK, long_idx, optarg, 1);
 		} else if (c == 0 && long_idx == 24) { // --heap-sort
-			if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
-				opt.flag |= MM_F_HEAP_SORT;
-			else opt.flag &= ~MM_F_HEAP_SORT;
+			yes_or_no(&opt, MM_F_HEAP_SORT, long_idx, optarg, 1);
+		} else if (c == 0 && long_idx == 26) { // --dual
+			yes_or_no(&opt, MM_F_NO_DUAL, long_idx, optarg, 0);
 		} else if (c == 'S') {
 			opt.flag |= MM_F_OUT_CS | MM_F_CIGAR | MM_F_OUT_CS_LONG;
 			if (mm_verbose >= 2)
@@ -261,8 +271,8 @@ int main(int argc, char *argv[])
 		fprintf(fp_help, "                 map-ont: -k15 (Oxford Nanopore vs reference mapping)\n");
 		fprintf(fp_help, "                 asm5: -k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 (asm to ref mapping; break at 5%% div.)\n");
 		fprintf(fp_help, "                 asm10: -k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 (asm to ref mapping; break at 10%% div.)\n");
-		fprintf(fp_help, "                 ava-pb: -Hk19 -w5 -Xp0 -m100 -g10000 --max-chain-skip 25 (PacBio read overlap)\n");
-		fprintf(fp_help, "                 ava-ont: -k15 -w5 -Xp0 -m100 -g10000 --max-chain-skip 25 (ONT read overlap)\n");
+		fprintf(fp_help, "                 ava-pb: -Hk19 -Xw5 -m100 -g10000 --max-chain-skip 25 (PacBio read overlap)\n");
+		fprintf(fp_help, "                 ava-ont: -k15 -Xw5 -m100 -g10000 --max-chain-skip 25 (ONT read overlap)\n");
 		fprintf(fp_help, "                 splice: long-read spliced alignment (see minimap2.1 for details)\n");
 		fprintf(fp_help, "                 sr: short single-end reads without splicing (see minimap2.1 for details)\n");
 		fprintf(fp_help, "\nSee `man ./minimap2.1' for detailed description of command-line options.\n");

map.c

@@ -116,15 +116,15 @@ static mm_match_t *collect_matches(void *km, int *_n_m, int max_occ, const mm_id
 static inline int skip_seed(int flag, uint64_t r, const mm_match_t *q, const char *qname, int qlen, const mm_idx_t *mi, int *is_self)
 {
 	*is_self = 0;
-	if (qname && (flag & (MM_F_NO_SELF|MM_F_AVA))) {
+	if (qname && (flag & (MM_F_NO_DIAG|MM_F_NO_DUAL))) {
 		const mm_idx_seq_t *s = &mi->seq[r>>32];
 		int cmp;
 		cmp = strcmp(qname, s->name);
-		if ((flag&MM_F_NO_SELF) && cmp == 0 && s->len == qlen) {
+		if ((flag&MM_F_NO_DIAG) && cmp == 0 && s->len == qlen) {
 			if ((uint32_t)r>>1 == (q->q_pos>>1)) return 1; // avoid the diagnonal anchors
 			if ((r&1) == (q->q_pos&1)) *is_self = 1; // this flag is used to avoid spurious extension on self chain
 		}
-		if ((flag&MM_F_AVA) && cmp > 0) // all-vs-all mode: map once
+		if ((flag&MM_F_NO_DUAL) && cmp > 0) // all-vs-all mode: map once
 			return 1;
 	}
 	if (flag & (MM_F_FOR_ONLY|MM_F_REV_ONLY)) {
@@ -237,11 +237,11 @@ static mm128_t *collect_seed_hits(void *km, const mm_mapopt_t *opt, int max_occ,
 
 static void chain_post(const mm_mapopt_t *opt, int max_chain_gap_ref, const mm_idx_t *mi, void *km, int qlen, int n_segs, const int *qlens, int *n_regs, mm_reg1_t *regs, mm128_t *a)
 {
-	if (!(opt->flag & MM_F_AVA)) { // don't choose primary mapping(s) for read overlap
+	if (!(opt->flag & MM_F_ALL_CHAINS)) { // don't choose primary mapping(s)
 		mm_set_parent(km, opt->mask_level, *n_regs, regs, opt->a * 2 + opt->b);
 		if (n_segs <= 1) mm_select_sub(km, opt->pri_ratio, mi->k*2, opt->best_n, n_regs, regs);
 		else mm_select_sub_multi(km, opt->pri_ratio, 0.2f, 0.7f, max_chain_gap_ref, mi->k*2, opt->best_n, n_segs, qlens, n_regs, regs);
-		if (!(opt->flag & MM_F_SPLICE) && !(opt->flag & MM_F_SR) && !(opt->flag & MM_F_NO_LJOIN))
+		if (!(opt->flag & (MM_F_SPLICE|MM_F_SR|MM_F_NO_LJOIN))) // long join not working well without primary chains
 			mm_join_long(km, opt, qlen, n_regs, regs, a);
 	}
 }
@@ -250,7 +250,7 @@ static mm_reg1_t *align_regs(const mm_mapopt_t *opt, const mm_idx_t *mi, void *k
 {
 	if (!(opt->flag & MM_F_CIGAR)) return regs;
 	regs = mm_align_skeleton(km, opt, mi, qlen, seq, n_regs, regs, a); // this calls mm_filter_regs()
-	if (!(opt->flag & MM_F_AVA)) {
+	if (!(opt->flag & MM_F_ALL_CHAINS)) { // don't choose primary mapping(s)
 		mm_set_parent(km, opt->mask_level, *n_regs, regs, opt->a * 2 + opt->b);
 		mm_select_sub(km, opt->pri_ratio, mi->k*2, opt->best_n, n_regs, regs);
 		mm_set_sam_pri(*n_regs, regs);

minimap.h

@@ -5,20 +5,20 @@
 #include <stdio.h>
 #include <sys/types.h>
 
-#define MM_F_NO_SELF     0x001
-#define MM_F_AVA         0x002
-#define MM_F_CIGAR       0x004
-#define MM_F_OUT_SAM     0x008
-#define MM_F_NO_QUAL     0x010
-#define MM_F_OUT_CG      0x020
-#define MM_F_OUT_CS      0x040
-#define MM_F_SPLICE      0x080 // splice mode
-#define MM_F_SPLICE_FOR  0x100 // match GT-AG
-#define MM_F_SPLICE_REV  0x200 // match CT-AC, the reverse complement of GT-AG
-#define MM_F_NO_LJOIN    0x400
-#define MM_F_OUT_CS_LONG 0x800
-#define MM_F_SR          0x1000
-#define MM_F_FRAG_MODE   0x2000
+#define MM_F_NO_DIAG       0x001 // no exact diagonal hit
+#define MM_F_NO_DUAL       0x002 // skip pairs where query name is lexicographically larger than target name
+#define MM_F_CIGAR         0x004
+#define MM_F_OUT_SAM       0x008
+#define MM_F_NO_QUAL       0x010
+#define MM_F_OUT_CG        0x020
+#define MM_F_OUT_CS        0x040
+#define MM_F_SPLICE        0x080 // splice mode
+#define MM_F_SPLICE_FOR    0x100 // match GT-AG
+#define MM_F_SPLICE_REV    0x200 // match CT-AC, the reverse complement of GT-AG
+#define MM_F_NO_LJOIN      0x400
+#define MM_F_OUT_CS_LONG   0x800
+#define MM_F_SR            0x1000
+#define MM_F_FRAG_MODE     0x2000
 #define MM_F_NO_PRINT_2ND  0x4000
 #define MM_F_2_IO_THREADS  0x8000
 #define MM_F_LONG_CIGAR    0x10000
@@ -28,6 +28,7 @@
 #define MM_F_FOR_ONLY      0x100000
 #define MM_F_REV_ONLY      0x200000
 #define MM_F_HEAP_SORT     0x400000
+#define MM_F_ALL_CHAINS    0x800000
 
 #define MM_I_HPC          0x1
 #define MM_I_NO_SEQ       0x2

minimap2.1

@@ -1,4 +1,4 @@
-.TH minimap2 1 "26 January 2018" "minimap2-2.7-dirty (r664)" "Bioinformatics tools"
+.TH minimap2 1 "31 January 2018" "minimap2-2.8-dirty (r671)" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences
@@ -129,7 +129,7 @@ Ignore top
 fraction of most frequent minimizers [0.0002]
 .TP
 .BI -g \ INT
-Stop chain enlongation if there are no minimizers in
+Stop chain enlongation if there are no minimizers within
 .IR INT -bp
 [10000].
 .TP
@@ -148,11 +148,28 @@ Discard chains with chaining score
 [40]. Chaining score equals the approximate number of matching bases minus a
 concave gap penalty. It is computed with dynamic programming.
 .TP
+.B -D
+If query sequence name/length are identical to the target name/length, ignore
+diagonal anchors. This option also reduces DP-based extension along the
+diagonal.
+.TP
+.B -P
+Retain all chains and don't attempt to set primary chains. Options
+.B -p
+and
+.B -N
+have no effect when this option is in use.
+.TP
+.BR --dual = yes | no
+During chaining, whether to skip pairs wherein the query name is
+lexicographically greater than the target name [yes]
+.TP
 .B -X
-Perform all-vs-all mapping. In this mode, if the query sequence name is
-lexicographically larger than the target sequence name, the hits between them
-will be suppressed; if the query sequence name is the same as the target name,
-diagonal minimizer hits will also be suppressed.
+Equivalent to
+.RB ' -DP
+.BR --dual = no
+.BR --no-long-join '.
+Primarily used for all-vs-all read overlapping.
 .TP
 .BI -p \ FLOAT
 Minimal secondary-to-primary score ratio to output secondary mappings [0.8].
@@ -162,6 +179,9 @@ the chain with a lower score is secondary to the chain with a higher score.
 If the ratio of the scores is below
 .IR FLOAT ,
 the secondary chain will not be outputted or extended with DP alignment later.
+This option has no effect when
+.B -X
+is applied.
 .TP
 .BI -N \ INT
 Output at most
@@ -179,7 +199,7 @@ Increasing this option slows down spliced alignment. [200k]
 .TP
 .BI -F \ NUM
 Maximum fragment length (aka insert size; effective with
-.BR -xsr / --frag)
+.BR -xsr / --frag = yes )
 [800]
 .TP
 .BI -M \ FLOAT
@@ -209,7 +229,7 @@ applies a second round of chaining with a higher minimizer occurrence threshold
 if no good chain is found. In addition, minimap2 attempts to patch gaps between
 seeds with ungapped alignment.
 .TP
-.BR --frag [= no | yes ]
+.BR --frag = no | yes
 Whether to enable the fragment mode [no]
 .TP
 .B --for-only
@@ -220,7 +240,7 @@ strand of the reference and the second read to the reverse stand.
 .B --rev-only
 Only map to the reverse complement strand of the reference sequences.
 .TP
-.BR --heap-sort [= no | yes ]
+.BR --heap-sort = no | yes
 If yes, sort anchors with heap merge, instead of radix sort. Heap merge is
 faster for short reads, but slower for long reads. [no]
 .SS Alignment options
@@ -272,14 +292,13 @@ no attempt to match GT-AG [n]
 .BI --end-bonus \ INT
 Score bonus when alignment extends to the end of the query sequence [0].
 .TP
-.BR --splice-flank [= yes | no ]
+.BR --splice-flank = yes | no
 Assume the next base to a
 .B GT
 donor site tends to be A/G (91% in human and 92% in mouse) and the preceding
 base to a
 .B AG
-acceptor tends to be C/T [yes with
-.BR --splice ].
+acceptor tends to be C/T [no].
 This trend is evolutionarily conservative, all the way to S. cerevisiae
 (PMID:18688272). Specifying this option generally leads to higher junction
 accuracy by several percents, so it is applied by default with
@@ -369,7 +388,7 @@ K/M/G/k/m/g suffix is accepted. A large
 helps load balancing in the multi-threading mode, at the cost of increased
 memory.
 .TP
-.BR --secondary [= yes | no ]
+.BR --secondary = yes | no
 Whether to output secondary alignments [yes]
 .TP
 .B --version
@@ -416,13 +435,13 @@ Up to 10% sequence divergence.
 .B ava-pb
 PacBio all-vs-all overlap mapping
 .RB ( -Hk19
-.B -w5 -Xp0 -m100 -g10000 --max-chain-skip
+.B -Xw5 -m100 -g10000 --max-chain-skip
 .BR 25 ).
 .TP
 .B ava-ont
 Oxford Nanopore all-vs-all overlap mapping
 .RB ( -k15
-.B -w5 -Xp0 -m100 -g10000 --max-chain-skip
+.B -Xw5 -m100 -g10000 --max-chain-skip
 .BR 25 ).
 Similarly, the major difference from
 .B ava-pb
@@ -444,8 +463,8 @@ tag ignores introns to demote hits to pseudogenes.
 .B sr
 Short single-end reads without splicing
 .RB ( -k21
-.B -w11 --sr --frag -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20
-.B -s40 -g200 -2K50m --heap-sort
+.B -w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20
+.B -s40 -g200 -2K50m --heap-sort=yes
 .BR --secondary=no ).
 .RE
 .SS Miscellaneous options
@@ -539,8 +558,8 @@ where seed positions may be suboptimal. This should not be a big concern
 because even the optimal alignment may be wrong in such regions.
 .TP
 *
-Minimap2 requires SSE2 instructions to compile. It is possible to add
-non-SSE2 support, but it would make minimap2 slower by several times.
+Minimap2 requires SSE2 or NEON instructions to compile. It is possible to add
+non-SSE2/NEON support, but it would make minimap2 slower by several times.
 .SH SEE ALSO
 .PP
 miniasm(1), minimap(1), bwa(1).

options.c

@@ -58,11 +58,11 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
 		mm_mapopt_init(mo);
 	} else if (strcmp(preset, "ava-ont") == 0) {
 		io->flag = 0, io->k = 15, io->w = 5;
-		mo->flag |= MM_F_AVA | MM_F_NO_SELF;
+		mo->flag |= MM_F_ALL_CHAINS | MM_F_NO_DIAG | MM_F_NO_DUAL | MM_F_NO_LJOIN;
 		mo->min_chain_score = 100, mo->pri_ratio = 0.0f, mo->max_gap = 10000, mo->max_chain_skip = 25;
 	} else if (strcmp(preset, "ava-pb") == 0) {
 		io->flag |= MM_I_HPC, io->k = 19, io->w = 5;
-		mo->flag |= MM_F_AVA | MM_F_NO_SELF;
+		mo->flag |= MM_F_ALL_CHAINS | MM_F_NO_DIAG | MM_F_NO_DUAL | MM_F_NO_LJOIN;
 		mo->min_chain_score = 100, mo->pri_ratio = 0.0f, mo->max_gap = 10000, mo->max_chain_skip = 25;
 	} else if (strcmp(preset, "map10k") == 0 || strcmp(preset, "map-pb") == 0) {
 		io->flag |= MM_I_HPC, io->k = 19;