Merge branch 'dev'
This commit is contained in:
Heng Li
commit
fd42d30910
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@ -522,14 +522,15 @@ function read_ALT_sam(fn)
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function bwa_altgen(args)
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{
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var c, opt = { a:1, b:4, o:6, e:1, verbose:3 };
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var c, opt = { a:1, b:4, o:6, e:1, verbose:3, show_pri:false };
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while ((c = getopt(args, 'v:')) != null) {
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while ((c = getopt(args, 'pv:')) != null) {
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if (c == 'v') opt.verbose = parseInt(getopt.arg);
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else if (c == 'p') opt.show_pri = true;
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}
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if (args.length == getopt.ind) {
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print("Usage: k8 bwa-helper.js altgen <alt.sam> [aln.sam]");
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print("Usage: k8 bwa-helper.js altgen [-p] <alt.sam> [aln.sam]");
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exit(1);
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}
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@ -671,6 +672,7 @@ function bwa_altgen(args)
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for (var i = 0; i < hits.length; ++i) {
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if (opt.verbose >= 5) print(obj2str(hits[i]));
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if (hits[i].g != reported_g || i == reported_i) continue;
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if (!opt.show_pri && idx[hits[i].ctg] == null) continue;
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var s = [t[0], flag&0xf10, hits[i].ctg, hits[i].start+1, mapQ, hits[i].cigar, '*', 0, 0];
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// update name
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if (flag&0x40) s[0] += "/1";
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@ -689,71 +691,6 @@ function bwa_altgen(args)
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buf.destroy();
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}
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// This is in effect a simplified version of bwa_genalt().
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function bwa_altlift(args)
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{
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var opt = { a:1, b:4, o:6, e:1 };
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if (args.length == 0) {
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print("Usage: k8 bwa-helper.js altlift <alt-to-ref.sam> [aln.sam]");
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exit(1);
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}
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var idx = read_ALT_sam(args[0]);
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// process SAM
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var file = args.length >= 2? new File(args[1]) : new File();
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var buf = new Bytes();
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while (file.readline(buf) >= 0) {
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var m, line = buf.toString();
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if (line.charAt(0) == '@') {
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print(line);
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continue;
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}
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var t = line.split("\t");
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var NM = (m = /\tNM:i:(\d+)/.exec(line)) == null? '0' : m[1];
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var flag = parseInt(t[1]);
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var h = parse_hit([t[2], ((flag&16)?'-':'+') + t[3], t[5], NM], opt);
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// lift mapping positions to coordinates on the primary assembly
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var a = null;
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if (idx[h.ctg] != null)
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a = idx[h.ctg](h.start, h.end);
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if (a == null) a = [];
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// find the approximate position on the primary assembly
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var lifted = [];
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for (var j = 0; j < a.length; ++j) {
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var s, e;
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if (!a[j][4]) { // ALT is mapped to the forward strand of the primary assembly
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s = cigar2pos(a[j][6], h.start);
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e = cigar2pos(a[j][6], h.end - 1) + 1;
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} else {
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s = cigar2pos(a[j][6], a[j][2] - h.end);
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e = cigar2pos(a[j][6], a[j][2] - h.start - 1) + 1;
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}
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if (s < 0 || e < 0) continue; // read is mapped to clippings in the ALT-to-chr alignment
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s += a[j][5]; e += a[j][5];
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lifted.push([a[j][3], (h.rev!=a[j][4]), s, e]);
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}
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h.lifted = lifted;
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// generate lifted_str
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if (h.lifted && h.lifted.length) {
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var lifted = h.lifted;
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var u = '';
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for (var j = 0; j < lifted.length; ++j)
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u += lifted[j][0] + "," + lifted[j][2] + "," + lifted[j][3] + "," + (lifted[j][1]?'-':'+') + ";";
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h.lifted_str = u;
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} else h.lifted_str = null;
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// print
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if (h.lifted_str) t.push("lt:Z:" + h.lifted_str);
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print(t.join("\t"));
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}
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buf.destroy();
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file.close();
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}
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/*********************
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*** Main function ***
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*********************/
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@ -762,8 +699,7 @@ function main(args)
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{
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if (args.length == 0) {
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print("\nUsage: k8 bwa-helper.js <command> [arguments]\n");
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print("Commands: altlift add lt tag to show lifted position on the primary assembly");
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print(" altgen generate ALT alignments for ALT-unaware alignments\n");
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print("Commands: altgen generate ALT alignments for ALT-unaware alignments");
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print(" sam2pas convert SAM to pairwise alignment summary format (PAS)");
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print(" pas2reg extract covered regions");
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print(" reg2cut regions to extract for the 2nd round bwa-mem");
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@ -780,8 +716,7 @@ function main(args)
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else if (cmd == 'markovlp') bwa_markOvlp(args);
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else if (cmd == 'pas2reg') bwa_pas2reg(args);
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else if (cmd == 'reg2cut') bwa_reg2cut(args);
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else if (cmd == 'altgen' || cmd == 'genalt') bwa_alt(args);
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else if (cmd == 'altlift') bwa_altlift(args);
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else if (cmd == 'altgen' || cmd == 'genalt') bwa_altgen(args);
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else if (cmd == 'shortname') bwa_shortname(args);
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else warn("Unrecognized command");
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}
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35
bwamem.c
35
bwamem.c
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@ -72,7 +72,8 @@ mem_opt_t *mem_opt_init()
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o->split_factor = 1.5;
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o->chunk_size = 10000000;
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o->n_threads = 1;
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o->max_hits = 5;
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o->max_XA_hits = 5;
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o->max_XA_hits_alt = 50;
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o->max_matesw = 50;
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o->mask_level_redun = 0.95;
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o->min_chain_weight = 0;
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@ -511,26 +512,38 @@ static void mem_mark_primary_se_core(const mem_opt_t *opt, int n, mem_alnreg_t *
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int mem_mark_primary_se(const mem_opt_t *opt, int n, mem_alnreg_t *a, int64_t id)
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{
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int i, n_pri;
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int i, j, n_pri;
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int_v z = {0,0,0};
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if (n == 0) return 0;
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for (i = n_pri = 0; i < n; ++i) {
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a[i].sub = 0, a[i].alt_sc = 0, a[i].secondary = -1, a[i].hash = hash_64(id+i);
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a[i].sub = a[i].alt_sc = 0, a[i].secondary = a[i].secondary_alt = -1, a[i].hash = hash_64(id+i);
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if (!a[i].is_alt) ++n_pri;
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}
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ks_introsort(mem_ars_hash, n, a);
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mem_mark_primary_se_core(opt, n, a, &z);
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for (i = 0; i < n; ++i) {
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mem_alnreg_t *p = &a[i];
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if (p->is_alt && p->secondary >= 0) // don't track the "parent" hit of ALT secondary hits
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p->secondary = INT_MAX;
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p->secondary_alt = i; // keep the rank in the first round
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if (!p->is_alt && p->secondary >= 0 && a[p->secondary].is_alt)
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p->alt_sc = a[p->secondary].score;
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}
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if (n_pri > 0 && n_pri < n) {
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ks_introsort(mem_ars_hash2, n, a);
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for (i = 0; i < n_pri; ++i) a[i].sub = 0, a[i].secondary = -1;
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mem_mark_primary_se_core(opt, n_pri, a, &z);
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if (n_pri >= 0 && n_pri < n) {
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kv_resize(int, z, n);
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if (n_pri > 0) ks_introsort(mem_ars_hash2, n, a);
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for (i = 0; i < n; ++i) z.a[a[i].secondary_alt] = i;
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for (i = 0; i < n; ++i) {
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if (a[i].secondary < 0) {
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a[i].secondary_alt = -1;
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continue;
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}
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j = z.a[a[i].secondary];
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a[i].secondary_alt = a[j].is_alt? j : -1;
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if (a[i].is_alt) a[i].secondary = INT_MAX;
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}
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if (n_pri > 0) { // mark primary for hits to the primary assembly only
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for (i = 0; i < n_pri; ++i) a[i].sub = 0, a[i].secondary = -1;
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mem_mark_primary_se_core(opt, n_pri, a, &z);
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}
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}
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free(z.a);
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return n_pri;
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@ -817,7 +830,7 @@ void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq
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if (p->n_cigar) { // aligned
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for (i = 0; i < p->n_cigar; ++i) {
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int c = p->cigar[i]&0xf;
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if (!(opt->flag&MEM_F_SOFTCLIP) && (c == 3 || c == 4))
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if (!(opt->flag&MEM_F_SOFTCLIP) && !p->is_alt && (c == 3 || c == 4))
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c = which? 4 : 3; // use hard clipping for supplementary alignments
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kputw(p->cigar[i]>>4, str); kputc("MIDSH"[c], str);
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}
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@ -976,7 +989,7 @@ void mem_reg2sam(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac,
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if (p->secondary >= 0) q->sub = -1; // don't output sub-optimal score
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if (k && p->secondary < 0) // if supplementary
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q->flag |= (opt->flag&MEM_F_NO_MULTI)? 0x10000 : 0x800;
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if (k && q->mapq > aa.a[0].mapq) q->mapq = aa.a[0].mapq;
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if (k && !p->is_alt && q->mapq > aa.a[0].mapq) q->mapq = aa.a[0].mapq;
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}
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if (aa.n == 0) { // no alignments good enough; then write an unaligned record
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mem_aln_t t;
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3
bwamem.h
3
bwamem.h
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@ -52,7 +52,7 @@ typedef struct {
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int mapQ_coef_fac;
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int max_ins; // when estimating insert size distribution, skip pairs with insert longer than this value
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int max_matesw; // perform maximally max_matesw rounds of mate-SW for each end
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int max_hits; // if there are max_hits or fewer, output them all
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int max_XA_hits, max_XA_hits_alt; // if there are max_hits or fewer, output them all
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int8_t mat[25]; // scoring matrix; mat[0] == 0 if unset
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} mem_opt_t;
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@ -69,6 +69,7 @@ typedef struct {
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int w; // actual band width used in extension
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int seedcov; // length of regions coverged by seeds
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int secondary; // index of the parent hit shadowing the current hit; <0 if primary
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int secondary_alt;
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int seedlen0; // length of the starting seed
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int n_comp:30, is_alt:2; // number of sub-alignments chained together
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float frac_rep;
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@ -112,43 +112,54 @@ void mem_reg2ovlp(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac,
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s->sam = str.s;
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}
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static inline void get_pri_idx(double XA_drop_ratio, const mem_alnreg_t *a, int i, int r[2])
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{
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int j = a[i].secondary, k = a[i].secondary_alt;
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r[0] = r[1] = -1;
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if (j >= 0 && j < INT_MAX && !a[j].is_alt && !a[i].is_alt && a[i].score >= a[j].score * XA_drop_ratio) r[0] = j;
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if (k >= 0 && a[k].is_alt && a[i].score >= a[k].score * XA_drop_ratio) r[1] = k;
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}
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// Okay, returning strings is bad, but this has happened a lot elsewhere. If I have time, I need serious code cleanup.
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char **mem_gen_alt(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, const mem_alnreg_v *a, int l_query, const char *query) // ONLY work after mem_mark_primary_se()
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{
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int i, k, *cnt, tot;
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kstring_t *aln = 0;
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int i, k, *cnt, tot, r[2];
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kstring_t *aln = 0, str = {0,0,0};
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char **XA = 0;
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cnt = calloc(a->n, sizeof(int));
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for (i = 0, tot = 0; i < a->n; ++i) {
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int j = a->a[i].secondary;
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if (j >= 0 && j < INT_MAX && a->a[i].score >= a->a[j].score * opt->XA_drop_ratio)
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++cnt[j], ++tot;
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get_pri_idx(opt->XA_drop_ratio, a->a, i, r);
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if (r[0] >= 0) ++cnt[r[0]], ++tot;
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if (r[1] >= 0) ++cnt[r[1]], ++tot;
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}
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if (tot == 0) goto end_gen_alt;
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aln = calloc(a->n, sizeof(kstring_t));
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for (i = 0; i < a->n; ++i) {
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mem_aln_t t;
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int j = a->a[i].secondary;
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if (j < 0 || j == INT_MAX || a->a[i].score < a->a[j].score * opt->XA_drop_ratio) continue; // we don't process the primary alignments as they will be converted to SAM later
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if (cnt[j] > opt->max_hits) continue;
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get_pri_idx(opt->XA_drop_ratio, a->a, i, r);
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if (r[0] < 0 && r[1] < 0) continue;
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if ((r[0] >= 0 && cnt[r[0]] > opt->max_XA_hits) || (r[1] >= 0 && cnt[r[1]] > opt->max_XA_hits_alt)) continue;
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t = mem_reg2aln(opt, bns, pac, l_query, query, &a->a[i]);
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kputs(bns->anns[t.rid].name, &aln[j]);
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kputc(',', &aln[j]); kputc("+-"[t.is_rev], &aln[j]); kputl(t.pos + 1, &aln[j]);
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kputc(',', &aln[j]);
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str.l = 0;
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kputs(bns->anns[t.rid].name, &str);
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kputc(',', &str); kputc("+-"[t.is_rev], &str); kputl(t.pos + 1, &str);
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kputc(',', &str);
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for (k = 0; k < t.n_cigar; ++k) {
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kputw(t.cigar[k]>>4, &aln[j]);
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kputc("MIDSHN"[t.cigar[k]&0xf], &aln[j]);
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kputw(t.cigar[k]>>4, &str);
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kputc("MIDSHN"[t.cigar[k]&0xf], &str);
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}
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kputc(',', &aln[j]); kputw(t.NM, &aln[j]);
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kputc(';', &aln[j]);
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kputc(',', &str); kputw(t.NM, &str);
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kputc(';', &str);
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free(t.cigar);
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if (r[0] >= 0 && cnt[r[0]] <= opt->max_XA_hits) kputsn(str.s, str.l, &aln[r[0]]);
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if (r[1] >= 0 && cnt[r[1]] <= opt->max_XA_hits_alt) kputsn(str.s, str.l, &aln[r[1]]);
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}
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XA = calloc(a->n, sizeof(char*));
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for (k = 0; k < a->n; ++k)
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XA[k] = aln[k].s;
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end_gen_alt:
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free(cnt); free(aln);
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free(cnt); free(aln); free(str.s);
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return XA;
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}
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@ -79,7 +79,6 @@ int main_mem(int argc, char *argv[])
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else if (c == 'r') opt->split_factor = atof(optarg), opt0.split_factor = 1.;
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else if (c == 'D') opt->drop_ratio = atof(optarg), opt0.drop_ratio = 1.;
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else if (c == 'm') opt->max_matesw = atoi(optarg), opt0.max_matesw = 1;
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else if (c == 'h') opt->max_hits = atoi(optarg), opt0.max_hits = 1;
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else if (c == 's') opt->split_width = atoi(optarg), opt0.split_width = 1;
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else if (c == 'G') opt->max_chain_gap = atoi(optarg), opt0.max_chain_gap = 1;
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else if (c == 'N') opt->max_chain_extend = atoi(optarg), opt0.max_chain_extend = 1;
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@ -88,6 +87,12 @@ int main_mem(int argc, char *argv[])
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else if (c == 'g') opt->min_pa_ratio = atof(optarg), opt0.min_pa_ratio = 1;
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else if (c == 'C') copy_comment = 1;
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else if (c == 'K') fixed_chunk_size = atoi(optarg);
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else if (c == 'h') {
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opt0.max_XA_hits = opt0.max_XA_hits_alt = 1;
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opt->max_XA_hits = opt->max_XA_hits_alt = strtol(optarg, &p, 10);
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if (*p != 0 && ispunct(*p) && isdigit(p[1]))
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opt->max_XA_hits_alt = strtol(p+1, &p, 10);
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}
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else if (c == 'Q') {
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opt0.mapQ_coef_len = 1;
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opt->mapQ_coef_len = atoi(optarg);
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@ -167,7 +172,7 @@ int main_mem(int argc, char *argv[])
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fprintf(stderr, " -v INT verbose level: 1=error, 2=warning, 3=message, 4+=debugging [%d]\n", bwa_verbose);
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fprintf(stderr, " -g FLOAT set mapQ to zero if the ratio of the primary-to-alt scores below FLOAT [%.3f]\n", opt->min_pa_ratio);
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fprintf(stderr, " -T INT minimum score to output [%d]\n", opt->T);
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fprintf(stderr, " -h INT if there are <INT hits with score >80%% of the max score, output all in XA [%d]\n", opt->max_hits);
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fprintf(stderr, " -h INT[,INT] if there are <INT hits with score >80%% of the max score, output all in XA [%d,%d]\n", opt->max_XA_hits, opt->max_XA_hits_alt);
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fprintf(stderr, " -a output all alignments for SE or unpaired PE\n");
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fprintf(stderr, " -C append FASTA/FASTQ comment to SAM output\n");
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fprintf(stderr, " -V output the reference FASTA header in the XR tag\n");
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