ruby-minigraph 0.0.20.0

data/ext/minigraph/tex/plots/CHM13-f1-90.bb.anno.gp

@@ -0,0 +1,42 @@
+#set t pdfcairo transparent enh font "Helvetica,15"
+set t po eps co so enh "Helvetica,18"
+
+set style line 1 lt 1 lc rgb "#FF0000" lw 1;
+set style line 2 lt 1 lc rgb "#00C000" lw 1;
+set style line 3 lt 1 lc rgb "#0080FF" lw 1;
+set style line 4 lt 1 lc rgb "#C000FF" lw 1;
+set style line 5 lt 1 lc rgb "#00EEEE" lw 1;
+set style line 6 lt 1 lc rgb "#FF80FF" lw 1;
+
+set style line 1 lt 1 lc rgb "#fbb4ae" lw 1;
+set style line 2 lt 1 lc rgb "#b3cde3" lw 1;
+set style line 3 lt 1 lc rgb "#ccebc5" lw 1;
+
+set out "CHM13-f1-90.bb.anno.cnt.eps"
+
+set size 1,0.9
+
+set style histogram rowstacked
+set xtics rotate by 40 right nomirror font "Helvetica,18"
+set boxwidth 0.8 relative
+set style data histograms
+set style fill solid 1.0 border lt -1
+#set style fill pattern 7 border lt -1
+set ylab "Count ({/Symbol \264}10^3)" off +0.0,0
+set bmargin 5
+set lmargin 8
+
+set title "CHM13 minigraph (CHM13 +GRCh38 +44 samples)"
+plot \
+	"<cat CHM13-f1-90.bb.anno.tbl" u ($3*1e-3):xtic(2) t '2 alleles' ls 1, \
+	"" u ($4*1e-3) t '3 alleles' ls 3, \
+	"" u ($5*1e-3) t '>3 alleles' ls 2
+
+set out "CHM13-f1-90.bb.anno.len.eps"
+
+set ylab "Sum of length on reference (Mbp)" off +0.0,0
+set key top left
+plot \
+	"<cat CHM13-f1-90.bb.anno.tbl" u ($6*1e-6):xtic(2) t '2 alleles' ls 1, \
+	"" u ($7*1e-6) t '3 alleles' ls 3, \
+	"" u ($8*1e-6) t '>3 alleles' ls 2

data/ext/minigraph/tex/plots/CHM13-f1-90.bb.anno.tbl

@@ -0,0 +1,13 @@
+01_Alu	Alu	14298	221	89	4354652	126178	114295
+02_L1	L1	3947	143	96	7536426	703699	642792
+03_SVA	SVA	1021	399	704	1240723	328180	995325
+04_ERV	ERV	1656	115	127	1009356	204523	1036717
+05_Mixed-MEI	Mixed-MEI	2088	251	137	4625357	1690752	2230499
+10_Satellite	Satellite	3619	747	1109	4148105	3066920	45077097
+11_VNTR	VNTR	5852	4010	8866	737321	838607	11642589
+12_STR	STR	4449	2178	910	392351	252638	879580
+13_Other-LCR	Other-LCR	3882	791	682	388838	159218	2049820
+20_Mixed-repeat	Mixed-repeat	848	185	336	2145808	1171839	7487870
+21_Partial-repeat	Partial-repeat	5240	613	760	13853718	6197517	26833676
+30_Non-rep-uniq	Non-rep-uniq	9175	501	130	788608	73912	43045
+31_Non-rep-dup	Non-rep-dup	878	177	333	441803	74941	1231962

data/ext/minigraph/tex/plots/CHM13-f1-90.bb.mini-inter-none.win.gp

@@ -0,0 +1,269 @@
+set t po eps co so enh "Helvetica,18"
+set out "chr-plot.eps"
+set size 2,1.52
+set multiplot layout 23,1
+set lmargin screen 0.095
+set border 0; unset xtics; unset ytics; set bmargin 0; set tmargin 0.02; set rmargin 0.02
+set style line 1 lc rgb "#377eb8" lw 1
+set style line 2 lc rgb "#e41a1c" lw 1
+set style line 3 lc rgb "#4daf4a" lw 1
+set yran [0:164]
+
+set style fill solid 0.8
+
+set origin 0,1.4447826086956521
+set xran [0:248.387497]
+set size 2,0.06521739130434782
+set style rect fc lt -1 fs solid 0.15 noborder
+unset obj; unset label
+set obj rect from 116.796216, graph 0 to 147.241828, graph 1
+set label "chr1" at screen 0.01, graph 0.5
+set key at screen 1.95,1.32
+plot \
+     "<awk '$1==\"chr1\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):(0):($3) t "VNTR" w filledcu ls 1, \
+     "<awk '$1==\"chr1\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3):($3+$4) not w filledcu ls 2, \
+     "<awk '$1==\"chr1\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3+$4):($3+$4+$5) not w filledcu ls 3
+set origin 0,1.3795652173913044
+set xran [0:242.696747]
+set size 1.95417845045558,0.06521739130434782
+set style rect fc lt -1 fs solid 0.15 noborder
+unset obj; unset label
+set obj rect from 85.991672, graph 0 to 99.67301599999999, graph 1
+set label "chr2" at screen 0.01, graph 0.5
+set key at screen 1.95,1.28
+plot \
+     "<awk '$1==\"chr2\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):(0):($3) not w filledcu ls 1, \
+     "<awk '$1==\"chr2\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3):($3+$4) t "Intersperse" w filledcu ls 2, \
+     "<awk '$1==\"chr2\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3+$4):($3+$4+$5) not w filledcu ls 3
+set origin 0,1.3143478260869565
+set xran [0:201.106605]
+set size 1.619297327191956,0.06521739130434782
+set style rect fc lt -1 fs solid 0.15 noborder
+unset obj; unset label
+set obj rect from 85.80519199999999, graph 0 to 101.415517, graph 1
+set label "chr3" at screen 0.01, graph 0.5
+set key at screen 1.95,1.24
+plot \
+     "<awk '$1==\"chr3\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):(0):($3) not w filledcu ls 1, \
+     "<awk '$1==\"chr3\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3):($3+$4) not w filledcu ls 2, \
+     "<awk '$1==\"chr3\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3+$4):($3+$4+$5) t "Partial/non-repeat" w filledcu ls 3
+set origin 0,1.2491304347826087
+set xran [0:193.57542999999998]
+set size 1.5586567950318369,0.06521739130434782
+set style rect fc lt -1 fs solid 0.15 noborder
+unset obj; unset label
+set obj rect from 44.705247, graph 0 to 59.870604, graph 1
+set label "chr4" at screen 0.01, graph 0.5
+plot \
+     "<awk '$1==\"chr4\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):(0):($3) not w filledcu ls 1, \
+     "<awk '$1==\"chr4\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3):($3+$4) not w filledcu ls 2, \
+     "<awk '$1==\"chr4\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3+$4):($3+$4+$5) not w filledcu ls 3
+set origin 0,1.1839130434782608
+set xran [0:182.045437]
+set size 1.4658180399474776,0.06521739130434782
+set style rect fc lt -1 fs solid 0.15 noborder
+unset obj; unset label
+set obj rect from 42.077197, graph 0 to 54.596619, graph 1
+set label "chr5" at screen 0.01, graph 0.5
+plot \
+     "<awk '$1==\"chr5\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):(0):($3) not w filledcu ls 1, \
+     "<awk '$1==\"chr5\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3):($3+$4) not w filledcu ls 2, \
+     "<awk '$1==\"chr5\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3+$4):($3+$4+$5) not w filledcu ls 3
+set origin 0,1.118695652173913
+set xran [0:172.12687]
+set size 1.3859543823979192,0.06521739130434782
+set style rect fc lt -1 fs solid 0.15 noborder
+unset obj; unset label
+set obj rect from 53.286919999999995, graph 0 to 66.058622, graph 1
+set label "chr6" at screen 0.01, graph 0.5
+plot \
+     "<awk '$1==\"chr6\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):(0):($3) not w filledcu ls 1, \
+     "<awk '$1==\"chr6\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3):($3+$4) not w filledcu ls 2, \
+     "<awk '$1==\"chr6\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3+$4):($3+$4+$5) not w filledcu ls 3
+set origin 0,1.0534782608695652
+set xran [0:160.567423]
+set size 1.2928784656177763,0.06521739130434782
+set style rect fc lt -1 fs solid 0.15 noborder
+unset obj; unset label
+set obj rect from 55.414367999999996, graph 0 to 68.714496, graph 1
+set label "chr7" at screen 0.01, graph 0.5
+plot \
+     "<awk '$1==\"chr7\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):(0):($3) not w filledcu ls 1, \
+     "<awk '$1==\"chr7\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3):($3+$4) not w filledcu ls 2, \
+     "<awk '$1==\"chr7\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3+$4):($3+$4+$5) not w filledcu ls 3
+set origin 0,0.9882608695652174
+set xran [0:146.259322]
+set size 1.1776705652780906,0.06521739130434782
+set style rect fc lt -1 fs solid 0.15 noborder
+unset obj; unset label
+set obj rect from 39.243541, graph 0 to 51.325075999999996, graph 1
+set label "chr8" at screen 0.01, graph 0.5
+plot \
+     "<awk '$1==\"chr8\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):(0):($3) not w filledcu ls 1, \
+     "<awk '$1==\"chr8\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3):($3+$4) not w filledcu ls 2, \
+     "<awk '$1==\"chr8\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3+$4):($3+$4+$5) not w filledcu ls 3
+set origin 0,0.9230434782608696
+set xran [0:150.61727399999998]
+set size 1.2127605118545883,0.06521739130434782
+set style rect fc lt -1 fs solid 0.15 noborder
+unset obj; unset label
+set obj rect from 39.952788999999996, graph 0 to 81.69403299999999, graph 1
+set label "chr9" at screen 0.01, graph 0.5
+plot \
+     "<awk '$1==\"chr9\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):(0):($3) not w filledcu ls 1, \
+     "<awk '$1==\"chr9\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3):($3+$4) not w filledcu ls 2, \
+     "<awk '$1==\"chr9\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3+$4):($3+$4+$5) not w filledcu ls 3
+set origin 0,0.8578260869565217
+set xran [0:134.758122]
+set size 1.0850636495604287,0.06521739130434782
+set style rect fc lt -1 fs solid 0.15 noborder
+unset obj; unset label
+set obj rect from 34.633784, graph 0 to 46.66458, graph 1
+set label "chr10" at screen 0.01, graph 0.5
+plot \
+     "<awk '$1==\"chr10\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):(0):($3) not w filledcu ls 1, \
+     "<awk '$1==\"chr10\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3):($3+$4) not w filledcu ls 2, \
+     "<awk '$1==\"chr10\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3+$4):($3+$4+$5) not w filledcu ls 3
+set origin 0,0.792608695652174
+set xran [0:135.127772]
+set size 1.0880400473619651,0.06521739130434782
+set style rect fc lt -1 fs solid 0.15 noborder
+unset obj; unset label
+set obj rect from 46.061948, graph 0 to 59.413484999999994, graph 1
+set label "chr11" at screen 0.01, graph 0.5
+plot \
+     "<awk '$1==\"chr11\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):(0):($3) not w filledcu ls 1, \
+     "<awk '$1==\"chr11\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3):($3+$4) not w filledcu ls 2, \
+     "<awk '$1==\"chr11\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3+$4):($3+$4+$5) not w filledcu ls 3
+set origin 0,0.7273913043478262
+set xran [0:133.324781]
+set size 1.0735224808839714,0.06521739130434782
+set style rect fc lt -1 fs solid 0.15 noborder
+unset obj; unset label
+set obj rect from 29.62049, graph 0 to 42.202481999999996, graph 1
+set label "chr12" at screen 0.01, graph 0.5
+plot \
+     "<awk '$1==\"chr12\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):(0):($3) not w filledcu ls 1, \
+     "<awk '$1==\"chr12\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3):($3+$4) not w filledcu ls 2, \
+     "<awk '$1==\"chr12\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3+$4):($3+$4+$5) not w filledcu ls 3
+set origin 0,0.6621739130434783
+set xran [0:114.240146]
+set size 0.9198542388790205,0.06521739130434782
+set style rect fc lt -1 fs solid 0.15 noborder
+unset obj; unset label
+set obj rect from 0, graph 0 to 23.171058, graph 1
+set label "chr13" at screen 0.01, graph 0.5
+plot \
+     "<awk '$1==\"chr13\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):(0):($3) not w filledcu ls 1, \
+     "<awk '$1==\"chr13\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3):($3+$4) not w filledcu ls 2, \
+     "<awk '$1==\"chr13\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3+$4):($3+$4+$5) not w filledcu ls 3
+set origin 0,0.5969565217391305
+set xran [0:101.219177]
+set size 0.8150102418399908,0.06521739130434782
+set style rect fc lt -1 fs solid 0.15 noborder
+unset obj; unset label
+set obj rect from 0, graph 0 to 17.765925, graph 1
+set label "chr14" at screen 0.01, graph 0.5
+plot \
+     "<awk '$1==\"chr14\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):(0):($3) not w filledcu ls 1, \
+     "<awk '$1==\"chr14\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3):($3+$4) not w filledcu ls 2, \
+     "<awk '$1==\"chr14\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3+$4):($3+$4+$5) not w filledcu ls 3
+set origin 0,0.5317391304347826
+set xran [0:100.338308]
+set size 0.8079175418398777,0.06521739130434782
+set style rect fc lt -1 fs solid 0.15 noborder
+unset obj; unset label
+set obj rect from 0, graph 0 to 23.279251, graph 1
+set label "chr15" at screen 0.01, graph 0.5
+plot \
+     "<awk '$1==\"chr15\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):(0):($3) not w filledcu ls 1, \
+     "<awk '$1==\"chr15\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3):($3+$4) not w filledcu ls 2, \
+     "<awk '$1==\"chr15\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3+$4):($3+$4+$5) not w filledcu ls 3
+set origin 0,0.4665217391304348
+set xran [0:96.33049299999999]
+set size 0.7756468756557421,0.06521739130434782
+set style rect fc lt -1 fs solid 0.15 noborder
+unset obj; unset label
+set obj rect from 30.848291, graph 0 to 57.219476, graph 1
+set label "chr16" at screen 0.01, graph 0.5
+plot \
+     "<awk '$1==\"chr16\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):(0):($3) not w filledcu ls 1, \
+     "<awk '$1==\"chr16\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3):($3+$4) not w filledcu ls 2, \
+     "<awk '$1==\"chr16\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3+$4):($3+$4+$5) not w filledcu ls 3
+set origin 0,0.4013043478260869
+set xran [0:84.277185]
+set size 0.6785944221661044,0.06521739130434782
+set style rect fc lt -1 fs solid 0.15 noborder
+unset obj; unset label
+set obj rect from 18.892709999999997, graph 0 to 32.48723, graph 1
+set label "chr17" at screen 0.01, graph 0.5
+plot \
+     "<awk '$1==\"chr17\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):(0):($3) not w filledcu ls 1, \
+     "<awk '$1==\"chr17\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3):($3+$4) not w filledcu ls 2, \
+     "<awk '$1==\"chr17\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3+$4):($3+$4+$5) not w filledcu ls 3
+set origin 0,0.33608695652173926
+set xran [0:80.542536]
+set size 0.6485232708794517,0.06521739130434782
+set style rect fc lt -1 fs solid 0.15 noborder
+unset obj; unset label
+set obj rect from 10.965698, graph 0 to 25.93355, graph 1
+set label "chr18" at screen 0.01, graph 0.5
+plot \
+     "<awk '$1==\"chr18\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):(0):($3) not w filledcu ls 1, \
+     "<awk '$1==\"chr18\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3):($3+$4) not w filledcu ls 2, \
+     "<awk '$1==\"chr18\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3+$4):($3+$4+$5) not w filledcu ls 3
+set origin 0,0.27086956521739136
+set xran [0:61.707359]
+set size 0.4968636484951576,0.06521739130434782
+set style rect fc lt -1 fs solid 0.15 noborder
+unset obj; unset label
+set obj rect from 19.655572, graph 0 to 34.768167999999996, graph 1
+set label "chr19" at screen 0.01, graph 0.5
+plot \
+     "<awk '$1==\"chr19\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):(0):($3) not w filledcu ls 1, \
+     "<awk '$1==\"chr19\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3):($3+$4) not w filledcu ls 2, \
+     "<awk '$1==\"chr19\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3+$4):($3+$4+$5) not w filledcu ls 3
+set origin 0,0.20565217391304347
+set xran [0:66.210247]
+set size 0.5331206103341023,0.06521739130434782
+set style rect fc lt -1 fs solid 0.15 noborder
+unset obj; unset label
+set obj rect from 21.383653, graph 0 to 37.969530999999996, graph 1
+set label "chr20" at screen 0.01, graph 0.5
+plot \
+     "<awk '$1==\"chr20\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):(0):($3) not w filledcu ls 1, \
+     "<awk '$1==\"chr20\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3):($3+$4) not w filledcu ls 2, \
+     "<awk '$1==\"chr20\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3+$4):($3+$4+$5) not w filledcu ls 3
+set origin 0,0.1404347826086958
+set xran [0:45.827690999999994]
+set size 0.3690015927009402,0.06521739130434782
+set style rect fc lt -1 fs solid 0.15 noborder
+unset obj; unset label
+set obj rect from 0, graph 0 to 17.078862, graph 1
+set label "chr21" at screen 0.01, graph 0.5
+plot \
+     "<awk '$1==\"chr21\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):(0):($3) not w filledcu ls 1, \
+     "<awk '$1==\"chr21\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3):($3+$4) not w filledcu ls 2, \
+     "<awk '$1==\"chr21\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3+$4):($3+$4+$5) not w filledcu ls 3
+set origin 0,0.07521739130434789
+set xran [0:51.353905999999995]
+set size 0.41349831710732204,0.06521739130434782
+set style rect fc lt -1 fs solid 0.15 noborder
+unset obj; unset label
+set obj rect from 0, graph 0 to 20.739832999999997, graph 1
+set label "chr22" at screen 0.01, graph 0.5
+plot \
+     "<awk '$1==\"chr22\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):(0):($3) not w filledcu ls 1, \
+     "<awk '$1==\"chr22\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3):($3+$4) not w filledcu ls 2, \
+     "<awk '$1==\"chr22\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3+$4):($3+$4+$5) not w filledcu ls 3
+set origin 0,0.01
+set xran [0:154.259625]
+set size 1.2420884856374232,0.06521739130434782
+set style rect fc lt -1 fs solid 0.15 noborder
+unset obj; unset label
+set obj rect from 52.820107, graph 0 to 65.927026, graph 1
+set label "chrX" at screen 0.01, graph 0.5
+plot \
+     "<awk '$1==\"chrX\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):(0):($3) not w filledcu ls 1, \
+     "<awk '$1==\"chrX\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3):($3+$4) not w filledcu ls 2, \
+     "<awk '$1==\"chrX\"' CHM13-f1-90.bb.mini-inter-none.win" u ($2*1e-6):($3+$4):($3+$4+$5) not w filledcu ls 3

data/ext/minigraph/tex/plots/CHM13-f1-90.bb.mini-inter-none.win.sh

@@ -0,0 +1,7 @@
+gzip -dc CHM13-f1-90.bb.anno.gz | awk '$12~/mini/' | ./bedutils.js window -l CHM13v1.size -w500000 -s100000 -c /dev/stdin > CHM13-f1-90.bb.mini-win
+gzip -dc CHM13-f1-90.bb.anno.gz | awk '$12~/inter|SINE|LINE|SVA|DNA|ERV/' | ./bedutils.js window -l CHM13v1.size -w500000 -s100000 -c /dev/stdin > CHM13-f1-90.bb.inter-win
+gzip -dc CHM13-f1-90.bb.anno.gz | awk '$12~/none|partial|self/' | ./bedutils.js window -l CHM13v1.size -w500000 -s100000 -c /dev/stdin > CHM13-f1-90.bb.none-win
+
+paste CHM13-f1-90.bb.mini-win CHM13-f1-90.bb.inter-win CHM13-f1-90.bb.none-win | awk '$1~/^chr([0-9]+|X)$/' | cut -f1-3,6,9 > CHM13-f1-90.bb.mini-inter-none.win
+
+./chr-plot.js -n3 CHM13v1.cen.bed CHM13-f1-90.bb.mini-inter-none.win|gnuplot

data/ext/minigraph/tex/plots/CHM13v1.cen.bed

@@ -0,0 +1,23 @@
+chr1	116796216	147241828	248387497
+chr2	85991672	99673016	242696747
+chr3	85805192	101415517	201106605
+chr4	44705247	59870604	193575430
+chr5	42077197	54596619	182045437
+chr6	53286920	66058622	172126870
+chr7	55414368	68714496	160567423
+chr8	39243541	51325076	146259322
+chr9	39952789	81694033	150617274
+chr10	34633784	46664580	134758122
+chr11	46061948	59413485	135127772
+chr12	29620490	42202482	133324781
+chr13	0	23171058	114240146
+chr14	0	17765925	101219177
+chr15	0	23279251	100338308
+chr16	30848291	57219476	96330493
+chr17	18892710	32487230	84277185
+chr18	10965698	25933550	80542536
+chr19	19655572	34768168	61707359
+chr20	21383653	37969531	66210247
+chr21	0	17078862	45827691
+chr22	0	20739833	51353906
+chrX	52820107	65927026	154259625

data/ext/minigraph/tex/plots/CHM13v1.size

@@ -0,0 +1,23 @@
+chr1	248387497
+chr2	242696747
+chr3	201106605
+chr4	193575430
+chr5	182045437
+chr6	172126870
+chr7	160567423
+chr8	146259322
+chr9	150617274
+chr10	134758122
+chr11	135127772
+chr12	133324781
+chr13	114240146
+chr14	101219177
+chr15	100338308
+chr16	96330493
+chr17	84277185
+chr18	80542536
+chr19	61707359
+chr20	66210247
+chr21	45827691
+chr22	51353906
+chrX	154259625

data/ext/minigraph/tex/plots/anno2tbl.js

@@ -0,0 +1,40 @@
+#!/usr/bin/env k8
+
+var buf = new Bytes();
+var file = arguments.length == 0? new File() : new File(arguments[0]);
+
+var h = {};
+while (file.readline(buf) >= 0) {
+	var t = buf.toString().split("\t");
+	for (var i = 1; i <= 7; ++i) t[i] = parseInt(t[i]);
+	if (t[5]) continue;
+	if (t[11] == "gap") continue;
+	if (/chrUn|_random/.test(t[0])) continue;
+	var na = t[4] < 4? t[4] : 4;
+	var type = null;
+	if (t[11] == "mini") type = "11_VNTR";
+	else if (t[11] == "micro") type = "12_STR";
+	else if (t[11] == "micro" || t[11] == "lcr") type = "13_Other-LCR";
+	else if (t[11] == "LINE/L1") type = "02_L1";
+	else if (t[11] == "SINE/Alu") type = "01_Alu";
+	else if (t[11] == "Retroposon/SVA") type = "03_SVA";
+	else if (t[11] == "LTR/ERV") type = "04_ERV";
+	else if (t[11] == "inter" || /^(DNA|LINE|SINE|LTR)/.test(t[11])) type = "05_Mixed-MEI";
+	else if (/^Satellite/.test(t[11]) || t[11] == "alpha" || t[11] == "hsat2/3") type = "10_Satellite";
+	else if (t[11] == "self") type = "31_Non-rep-dup";
+	else if (t[11] == "none") type = "30_Non-rep-uniq";
+	else if (t[11] == "mixed") type = "20_Mixed-repeat";
+	else type = "21_Partial-repeat";
+	var key = type;
+	if (h[key] == null) h[key] = [0, null, 0, 0, 0, 0, 0, 0];
+	++h[key][na];
+	h[key][na+3] += t[7];
+}
+
+file.close();
+buf.destroy();
+
+for (var key in h) {
+	var label = key.replace(/^[0-9]+_/, "");
+	print(key, label, h[key][2], h[key][3], h[key][4], h[key][5], h[key][6], h[key][7]);
+}