ruby-minigraph 0.0.20.0

data/ext/minigraph/tex/plots/bedutils.js

@@ -0,0 +1,367 @@
+#!/usr/bin/env k8
+
+/*****************************
+ ***** Library functions *****
+ *****************************/
+
+/*******************************
+ * Command line option parsing *
+ *******************************/
+
+var getopt = function(args, ostr) {
+	var oli; // option letter list index
+	if (typeof(getopt.place) == 'undefined')
+		getopt.ind = 0, getopt.arg = null, getopt.place = -1;
+	if (getopt.place == -1) { // update scanning pointer
+		if (getopt.ind >= args.length || args[getopt.ind].charAt(getopt.place = 0) != '-') {
+			getopt.place = -1;
+			return null;
+		}
+		if (getopt.place + 1 < args[getopt.ind].length && args[getopt.ind].charAt(++getopt.place) == '-') { // found "--"
+			++getopt.ind;
+			getopt.place = -1;
+			return null;
+		}
+	}
+	var optopt = args[getopt.ind].charAt(getopt.place++); // character checked for validity
+	if (optopt == ':' || (oli = ostr.indexOf(optopt)) < 0) {
+		if (optopt == '-') return null; //  if the user didn't specify '-' as an option, assume it means null.
+		if (getopt.place < 0) ++getopt.ind;
+		return '?';
+	}
+	if (oli+1 >= ostr.length || ostr.charAt(++oli) != ':') { // don't need argument
+		getopt.arg = null;
+		if (getopt.place < 0 || getopt.place >= args[getopt.ind].length) ++getopt.ind, getopt.place = -1;
+	} else { // need an argument
+		if (getopt.place >= 0 && getopt.place < args[getopt.ind].length)
+			getopt.arg = args[getopt.ind].substr(getopt.place);
+		else if (args.length <= ++getopt.ind) { // no arg
+			getopt.place = -1;
+			if (ostr.length > 0 && ostr.charAt(0) == ':') return ':';
+			return '?';
+		} else getopt.arg = args[getopt.ind]; // white space
+		getopt.place = -1;
+		++getopt.ind;
+	}
+	return optopt;
+}
+
+/***************
+ * BED overlap *
+ ***************/
+
+function it_index(a) {
+	if (a.length == 0) return -1;
+	a.sort(function(x, y) { return x[0] - y[0] });
+	var last, last_i;
+	for (var i = 0; i < a.length; i += 2) last = a[i][2] = a[i][1], last_i = i;
+	for (var k = 1; 1<<k <= a.length; ++k) {
+		var i0 = (1<<k) - 1, step = 1<<(k+1);
+		for (var i = i0; i < a.length; i += step) {
+			var x = 1<<(k-1);
+			a[i][2] = a[i][1];
+			if (a[i][2] < a[i-x][2]) a[i][2] = a[i-x][2];
+			var e = i + x < a.length? a[i+x][2] : last;
+			if (a[i][2] < e) a[i][2] = e;
+		}
+		last_i = last_i>>k&1? last_i - (1<<(k-1)) : last_i + (1<<(k-1));
+		if (last_i < a.length) last = last > a[last_i][2]? last : a[last_i][2];
+	}
+	return k - 1;
+}
+
+function it_overlap(a, st, en) {
+	var h, stack = [], b = [];
+	for (h = 0; 1<<h <= a.length; ++h);
+	--h;
+	stack.push([(1<<h) - 1, h, 0]);
+	while (stack.length) {
+		var t = stack.pop();
+		var x = t[0], h = t[1], w = t[2];
+		if (h <= 2) {
+			var i0 = x >> h << h, i1 = i0 + (1<<(h+1)) - 1;
+			if (i1 >= a.length) i1 = a.length;
+			for (var i = i0; i < i1; ++i)
+				if (a[i][0] < en && st < a[i][1])
+					b.push(i);
+		} else if (w == 0) { // if left child not processed
+			stack.push([x, h, 1]);
+			var y = x - (1<<(h-1));
+			if (y >= a.length || a[y][2] > st)
+				stack.push([y, h - 1, 0]);
+		} else if (x < a.length && a[x][0] < en) {
+			if (st < a[x][1]) b.push(x);
+			stack.push([x + (1<<(h-1)), h - 1, 0]);
+		}
+	}
+	return b;
+}
+
+/******************************
+ ***** Command-line tools *****
+ ******************************/
+
+function bed_sum(args)
+{
+	var buf = new Bytes();
+	var file = args.length == 0 || args[0] == '-'? new File() : new File(args[0]);
+	var s = 0;
+	while (file.readline(buf) >= 0) {
+		var t = buf.toString().split("\t", 3);
+		if (t.length < 3) continue;
+		s += parseInt(t[2])  - parseInt(t[1]);
+	}
+	file.close();
+	buf.destroy();
+	print(s);
+	return 0;
+}
+
+function bed_sum2nd(args)
+{
+	var buf = new Bytes();
+	var file = args.length == 0 || args[0] == '-'? new File() : new File(args[0]);
+	var s = 0;
+	while (file.readline(buf) >= 0) {
+		var t = buf.toString().split("\t", 2);
+		s += parseInt(t[1]);
+	}
+	file.close();
+	buf.destroy();
+	print(s);
+	return 0;
+}
+
+function bed_merge(args)
+{
+	var buf = new Bytes();
+	var file = args.length > 0? new File(args[0]) : new File();
+	var ctg = null, st, en;
+	while (file.readline(buf) >= 0) {
+		var t = buf.toString().split("\t", 3);
+		var s = parseInt(t[1]);
+		var e = parseInt(t[2]);
+		if (ctg != t[0] || s > en) { // no overlap
+			if (ctg != null) print(ctg, st, en);
+			ctg = t[0], st = s, en = e;
+		} else if (s < st) throw Error("ERROR: input is not sorted by coordinate");
+		else en = en > e? en : e;
+	}
+	if (ctg != null) print(ctg, st, en);
+	file.close();
+	buf.destroy();
+	return 0;
+}
+
+function bed_sum1(args)
+{
+	var buf = new Bytes();
+	var file = args.length == 0 || args[0] == '-'? new File() : new File(args[0]);
+	var ctg = null, st = 0, en = 0, sum = 0;
+	while (file.readline(buf) >= 0) {
+		var t = buf.toString().split("\t", 3);
+		var s = parseInt(t[1]);
+		var e = parseInt(t[2]);
+		if (ctg != t[0] || s > en) { // no overlap
+			sum += en - st;
+			if (ctg != null && ctg != t[0]) {
+				print(ctg, sum);
+				sum = 0;
+			}
+			ctg = t[0], st = s, en = e;
+		} else if (s < st) throw Error("ERROR: input is not sorted by coordinate");
+		else en = en > e? en : e;
+	}
+	if (ctg != null) {
+		sum += en - st;
+		print(ctg, sum);
+	}
+	file.close();
+	buf.destroy();
+	return 0;
+}
+
+function bed_gdist(args)
+{
+	if (args.length == 0) {
+		print("Usage: bedutils.js gdist <3-col-gmap.txt> <reg.bed>");
+		exit(1);
+	}
+	var file, buf = new Bytes();
+
+	var gmap = {};
+	file = new File(args[0]);
+	var last_pos = 0, last_ctg = null, last_v = 0.0;
+	while (file.readline(buf) >= 0) {
+		var t = buf.toString().split("\t");
+		var pos = parseInt(t[1]);
+		var v = parseFloat(t[2]);
+		if (last_ctg != t[0] && last_ctg != null) {
+			gmap[last_ctg].push([last_pos, 0x7fffffff, -1, last_v]);
+			last_pos = 0, last_v = 0.0;
+		}
+		if (gmap[t[0]] == null) gmap[t[0]] = [];
+		if (last_pos == pos) throw Error("Zero-length interval");
+		gmap[t[0]].push([last_pos, pos, -1, last_v]);
+		last_pos = pos, last_ctg = t[0], last_v = v;
+	}
+	if (last_ctg != null)
+		gmap[last_ctg].push([last_pos, 0x7fffffff, -1, last_v]);
+	file.close();
+
+	for (var ctg in gmap) it_index(gmap[ctg]);
+
+	file = args.length >= 2? new File(args[1]) : new File();
+	while (file.readline(buf) >= 0) {
+		var t = buf.toString().split("\t");
+		var st = parseInt(t[1]), en = parseInt(t[2]);
+		var v, g = gmap[t[0]];
+		if (g == null) v = -1;
+		else if (st == en) v = 0;
+		else {
+			var as = it_overlap(g, st, st + 1);
+			var ae = it_overlap(g, en - 1, en);
+			if (as.length != 1 || ae.length != 1)
+				throw Error("Bug!");
+			var is = as[0], ie = ae[0];
+			var xs = g[is][3] + (is == g.length - 1? 0 : (g[is+1][3] - g[is][3]) / (g[is][1] - g[is][0]) * (st - g[is][0]));
+			var xe = g[ie][3] + (ie == g.length - 1? 0 : (g[ie+1][3] - g[ie][3]) / (g[ie][1] - g[ie][0]) * (en - g[ie][0]));
+			v = 1e6 * (xe - xs) / (en - st);
+		}
+		v = v <= 0? v : v.toFixed(15);
+		print(t[0], t[1], t[2], v);
+	}
+	file.close();
+	buf.destroy();
+}
+
+function bed_window(args)
+{
+	var c, win_size = 1000000, skip = 500000, cnt_only = false, fn_len = null;
+	while ((c = getopt(args, "w:s:cl:")) != null) {
+		if (c == 'w') win_size = parseInt(getopt.arg);
+		else if (c == 's') skip = parseInt(getopt.arg);
+		else if (c == 'c') cnt_only = true;
+		else if (c == 'l') fn_len = getopt.arg;
+	}
+
+	var lens = {}, file, buf = new Bytes();
+	if (fn_len) {
+		file = new File(fn_len);
+		while (file.readline(buf) >= 0) {
+			var t = buf.toString().split("\t");
+			if (t.length < 2) continue;
+			lens[t[0]] = parseInt(t[1]);
+		}
+		file.close();
+	}
+	file = getopt.ind < args.length? new File(args[getopt.ind]) : new File();
+	var bed = {}, ctgs = [];
+	while (file.readline(buf) >= 0) {
+		var t = buf.toString().split("\t");
+		if (bed[t[0]] == null) { bed[t[0]] = []; ctgs.push(t[0]); }
+		bed[t[0]].push([parseInt(t[1]), parseInt(t[2]), -1]);
+	}
+	file.close();
+	buf.destroy();
+
+	for (var ct = 0; ct < ctgs.length; ++ct) {
+		var ctg = ctgs[ct];
+		it_index(bed[ctg]);
+		var a = bed[ctg];
+		var max = 0;
+		for (var i = 0; i < a.length; ++i)
+			max = max > a[i][1]? max : a[i][1];
+		if (lens[ctg] > 0 && max < lens[ctg]) max = lens[ctg];
+		for (var x = 0; x < max; x += skip) {
+			var st = x - (win_size>>1), en = x + (win_size>>1);
+			if (st < 0) st = 0;
+			if (en > max) en = max;
+			var sum = 0, b = it_overlap(a, st, en);
+			if (cnt_only) {
+				sum = b.length;
+			} else {
+				for (var i = 0; i < b.length; ++i) {
+					var c = a[b[i]];
+					var s = st > c[0]? st : c[0];
+					var e = en < c[1]? en : c[1];
+					sum += e - s;
+				}
+			}
+			print(ctg, x, sum/(en-st)*1e6);
+		}
+	}
+}
+
+function bed_cov(args)
+{
+	if (args.length < 2) {
+		warn("Usage: bedutils.js cov <loaded.bed> <streamed.bed>");
+		exit(1);
+	}
+	var file, buf = new Bytes();
+
+	file = new File(args[0]);
+	var bed = {};
+	while (file.readline(buf) >= 0) {
+		var t = buf.toString().split("\t", 3);
+		if (bed[t[0]] == null) bed[t[0]] = [];
+		bed[t[0]].push([parseInt(t[1]), parseInt(t[2])]);
+	}
+	for (var ctg in bed) it_index(bed[ctg]);
+	file.close();
+
+	file = new File(args[1]);
+	while (file.readline(buf) >= 0) {
+		var t = buf.toString().split("\t", 3);
+		if (bed[t[0]] == null) {
+			print(t[0], t[1], t[2], 0, 0);
+		} else {
+			var st0 = parseInt(t[1]), en0 = parseInt(t[2]);
+			var b = bed[t[0]];
+			var a = it_overlap(b, st0, en0);
+			var cov_st = 0, cov_en = 0, cov = 0;
+			for (var i = 0; i < a.length; ++i) {
+				var st1 = b[a[i]][0] > st0? b[a[i]][0] : st0;
+				var en1 = b[a[i]][1] < en0? b[a[i]][1] : en0;
+				if (st1 > cov_en) {
+					cov += cov_en - cov_st;
+					cov_st = st1, cov_en = en1;
+				} else cov_en = cov_en > en1? cov_en : en1;
+			}
+			cov += cov_en - cov_st;
+			print(t[0], t[1], t[2], a.length, cov);
+		}
+	}
+	file.close();
+
+	buf.destroy();
+}
+
+function main(args)
+{
+	if (args.length == 0) {
+		print("Usage: bedutils.js <command> [arguments]");
+		print("Commands:");
+		print("  sum        sum of BED regions (deprecated by bedtk)");
+		print("  sum1       sum of BED regions for each contig");
+		print("  sum2nd     sum of the 2nd column");
+		print("  merge      merge overlapping regions in *sorted* BED (deprecated)");
+		print("  cov        breadth of coverage (deprecated by bedtk)");
+		print("  gdist      genetic distance from 3-col genetic map");
+		print("  window     window-based counting");
+		exit(1);
+	}
+
+	var cmd = args.shift();
+	if (cmd == 'sum') bed_sum(args);
+	else if (cmd == 'sum2nd') bed_sum2nd(args);
+	else if (cmd == 'sum1') bed_sum1(args);
+	else if (cmd == 'merge') bed_merge(args);
+	else if (cmd == 'cov') bed_cov(args);
+	else if (cmd == 'gdist') bed_gdist(args);
+	else if (cmd == 'window') bed_window(args);
+	else throw Error("unrecognized command: " + cmd);
+}
+
+main(arguments);

data/ext/minigraph/tex/plots/chr-plot.js

@@ -0,0 +1,130 @@
+#!/usr/bin/env k8
+
+var getopt = function(args, ostr) {
+	var oli; // option letter list index
+	if (typeof(getopt.place) == 'undefined')
+		getopt.ind = 0, getopt.arg = null, getopt.place = -1;
+	if (getopt.place == -1) { // update scanning pointer
+		if (getopt.ind >= args.length || args[getopt.ind].charAt(getopt.place = 0) != '-') {
+			getopt.place = -1;
+			return null;
+		}
+		if (getopt.place + 1 < args[getopt.ind].length && args[getopt.ind].charAt(++getopt.place) == '-') { // found "--"
+			++getopt.ind;
+			getopt.place = -1;
+			return null;
+		}
+	}
+	var optopt = args[getopt.ind].charAt(getopt.place++); // character checked for validity
+	if (optopt == ':' || (oli = ostr.indexOf(optopt)) < 0) {
+		if (optopt == '-') return null; //  if the user didn't specify '-' as an option, assume it means null.
+		if (getopt.place < 0) ++getopt.ind;
+		return '?';
+	}
+	if (oli+1 >= ostr.length || ostr.charAt(++oli) != ':') { // don't need argument
+		getopt.arg = null;
+		if (getopt.place < 0 || getopt.place >= args[getopt.ind].length) ++getopt.ind, getopt.place = -1;
+	} else { // need an argument
+		if (getopt.place >= 0 && getopt.place < args[getopt.ind].length)
+			getopt.arg = args[getopt.ind].substr(getopt.place);
+		else if (args.length <= ++getopt.ind) { // no arg
+			getopt.place = -1;
+			if (ostr.length > 0 && ostr.charAt(0) == ':') return ':';
+			return '?';
+		} else getopt.arg = args[getopt.ind]; // white space
+		getopt.place = -1;
+		++getopt.ind;
+	}
+	return optopt;
+}
+
+var c, width = 2, height = 1.5, y_max0 = null, y_min0 = null, fn_out = "chr-plot.eps", n = 1, fsize = 14;
+while ((c = getopt(arguments, "w:h:x:i:o:n:f:")) != null) {
+	if (c == 'h') height = parseFloat(getopt.arg);
+	else if (c == 'n') n = parseInt(getopt.arg);
+	else if (c == 'w') width = parseFloat(getopt.arg);
+	else if (c == 'x') y_max0 = parseFloat(getopt.arg);
+	else if (c == 'i') y_min0 = parseFloat(getopt.arg);
+	else if (c == 'o') fn_out = getopt.arg;
+	else if (c == 'f') fsize = parseInt(getopt.arg);
+}
+
+if (arguments.length - getopt.ind < 2) {
+	print("Usage: chr-plot.js [options] <chr.size> <dat.txt>");
+	print("Options:");
+	print("  -n INT      number of data points [" + n + "]");
+	print("  -w FLOAT    width of the plot [" + width + "]");
+	print("  -h FLOAT    height of the plot [" + height + "]");
+	print("  -x FLOAT    max y value [auto]");
+	print("  -i FLOAT    min y value [auto]");
+	print("  -o FILE     output file name [chr-plot.eps]");
+	exit(1);
+}
+
+var file, buf = new Bytes();
+
+var chr_list = [], chr = {}, cen = [], max_len = 0;
+file = new File(arguments[getopt.ind]);
+while (file.readline(buf) >= 0) {
+	var t = buf.toString().split("\t");
+	var len = parseInt(t[3]);
+	chr_list.push(t[0]);
+	cen.push([parseInt(t[1]), parseInt(t[2])]);
+	chr[t[0]] = len;
+	max_len = max_len > len? max_len : len;
+}
+file.close();
+
+var y_max = -1e300, y_min = 1e300;
+file = new File(arguments[getopt.ind+1]);
+while (file.readline(buf) >= 0) {
+	var t = buf.toString().split("\t");
+	if (chr[t[0]] == null) continue;
+	var y = parseFloat(t[2]);
+	y_max = y_max > y? y_max : y;
+	y_min = y_min < y? y_min : y;
+}
+file.close();
+if (y_max0 != null) y_max = y_max0;
+if (y_min0 != null) y_min = y_min0;
+
+buf.destroy();
+
+print('set t po eps co so enh "Helvetica,' + fsize + '"');
+print('set out "' + fn_out + '"');
+print('set size ' + width + ',' + (height + 0.02));
+print('set multiplot layout ' + chr_list.length + ',1');
+print('set lmargin screen ' + (fsize/2 * 0.01 + 0.005).toFixed(3));
+print('set border 0; unset xtics; unset ytics; set bmargin 0; set tmargin 0.02; set rmargin 0.02');
+print('set style line 1 lc rgb "#377eb8" lw 1');
+print('set style line 2 lc rgb "#e41a1c" lw 1');
+print('set style line 3 lc rgb "#4daf4a" lw 1');
+//print('set style fill transparent solid 0.5 noborder');
+print('set yran [' + y_min + ':' + y_max + ']');
+print('');
+var h = height / chr_list.length;
+for (var i = 0; i < chr_list.length; ++i) {
+	var len = chr[chr_list[i]];
+	print('set origin 0,' + (height - (i + 1) * h + 0.01));
+	print('set xran [0:' + len * 1e-6 + ']');
+	print('set size ' + (width*len/max_len) + ',' + h);
+	print('set style rect fc lt -1 fs solid 0.15 noborder');
+	print('unset obj; unset label');
+	print('set obj rect from ' + cen[i][0]*1e-6 + ', graph 0 to ' + cen[i][1]*1e-6 + ', graph 1');
+	print('set label "' + chr_list[i] + '" at screen 0.01, graph 0.5');
+	print('plot \\');
+	for (var j = 0; j < n; ++j) {
+		var st, en, endl = j == n - 1? '' : ', \\';
+		if (j > 0) {
+			st = en = '';
+			for (var k = 0; k < j; ++k) {
+				st += '+$' + (k + 3);
+				en += '+$' + (k + 3);
+			}
+			en += '+$' + (j + 3);
+			st = st.replace(/^\+/, "(") + ")";
+			en = en.replace(/^\+/, "(") + ")";
+		} else st = '(0)', en = '($3)';
+		print('     "<awk \'$1==\\"' + chr_list[i] + '\\"\' ' + arguments[getopt.ind+1] + '" u ($2*1e-6):' + st + ':' + en + ' not w filledcu ls ' + (j+1) + endl);
+	}
+}

data/ext/minigraph/tex/plots/gen-anno.mak

@@ -0,0 +1,24 @@
+prefix=CHM13-f1-90.bb
+
+all:$(prefix).base $(prefix).gap $(prefix).brnn.gz $(prefix).etrf.gz $(prefix).sdust.gz
+
+$(prefix).base:$(prefix).fa
+	seqtk comp $< | cut -f1,2 | perl -ane 'print "$$1\t$$2\t$$3\t$$F[1]\n" if $$F[0]=~/(\S+)_(\d+)_(\d+)/' > $@
+
+$(prefix).gap:$(prefix).fa
+	seqtk gap $< > $@
+
+$(prefix).brnn.gz:$(prefix).fa
+	~/dna-nn/dna-brnn -Ai ~/dna-nn/attcc-alpha.knm -t16 $< | htsbox bgzip > $@
+
+$(prefix).etrf.gz:$(prefix).fa
+	~/src/etrf/etrf $< | htsbox bgzip > $@
+
+$(prefix).sdust.gz:$(prefix).fa
+	~/minimap2/sdust $< | htsbox bgzip > $@
+
+CHM13-f1-90.bb.paf.gz:CHM13-f1-90.bb.fa
+	minimap2 -cxasm20 -r2k --cs -t16 ~/ref/CHM13v1Y.fa $< 2> CHM13-f1-90.bb.paf.log | gzip > $@
+
+GRCh38-f1-90.bb.paf.gz:GRCh38-f1-90.bb.fa
+	minimap2 -cxasm20 -r2k --cs -t16 ~/ref/hs38.fa $< 2> GRCh38-f1-90.bb.paf.log | gzip > $@

data/ext/minigraph.patch

@@ -0,0 +1,21 @@
+--- a/Makefile
++++ b/Makefile
+@@ -1,11 +1,11 @@
+ CC=			gcc
+-CFLAGS=		-g -Wall -Wc++-compat -std=c99 -msse4 -O3
++CFLAGS=		-g -Wall -Wc++-compat -std=c99 -msse4 -O3 -fPIC
+ CPPFLAGS=
+ INCLUDES=
+ OBJS=		kalloc.o kthread.o algo.o sys.o gfa-base.o gfa-io.o gfa-aug.o gfa-bbl.o gfa-ed.o \
+             sketch.o misc.o bseq.o options.o shortk.o miniwfa.o \
+ 			index.o lchain.o gchain1.o galign.o gcmisc.o map-algo.o cal_cov.o \
+-			format.o gmap.o ggsimple.o ggen.o asm-call.o
++			format.o gmap.o ggsimple.o ggen.o asm-call.o cmappy.o
+ PROG=		minigraph
+ LIBS=		-lz -lpthread -lm
+ 
+@@ -64,3 +64,4 @@ options.o: mgpriv.h minigraph.h gfa.h sys.h
+ shortk.o: mgpriv.h minigraph.h gfa.h ksort.h kavl.h algo.h khashl.h kalloc.h
+ sketch.o: kvec-km.h kalloc.h mgpriv.h minigraph.h gfa.h
+ sys.o: sys.h
++cmappy.o: cmappy.h