# HG changeset patch
# User iuc
# Date 1512859023 18000
# Node ID 0802a40af216d57b2e60319e383f681bf9fba076

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/ commit 2d4c604c2e76baaf744748be3d56e5504a0184b7

diff -r 000000000000 -r 0802a40af216 swift.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/swift.xml	Sat Dec 09 17:37:03 2017 -0500
@@ -0,0 +1,135 @@
+<tool id="swiftlink" name="Swiftlink" version="@VERSION@.0" >
+    <description>Parallel MCMC Linkage Analysis</description>
+    <macros>
+        <token name="@VERSION@">1.0</token>
+        <xml name="test_inputs" >
+            <param name="inp_ped" value="pedin.21" />
+            <param name="inp_dat" value="datain.21" />
+            <param name="inp_map" value="map.21" />
+        </xml>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@VERSION@">swiftlink</requirement>
+        <requirement type="package" version="2017.3">linkage2allegro</requirement>
+    </requirements>
+    <!-- <version_command></version_command> Note: a version is never output by the program... -->
+    <command detect_errors='exit_code'><![CDATA[
+swiftlink
+ -p '${inp_ped}'
+ -m '${inp_map}'
+ -d '${inp_dat}'
+ ${misc.X}
+ ${misc.a}
+ -q ${misc.q}
+ -c \${GALAXY_SLOTS:-3}
+ -i ${mcmc.i}
+ -b ${mcmc.b}
+ -s ${mcmc.s}
+ -x ${mcmc.x}
+ -l ${mcmc.l}
+ -n ${mcmc.n}
+ -R ${mcmc.R}
+
+#if $misc.r
+    -r '${misc.r}'
+#end if
+
+#if $elod_opts.e == 'yes':   ## 'true' / 'false' as opt values parse badly
+    -e
+    -f $elod_opts.f
+    -w $elod_opts.w
+    -k '$elod_opts.k'
+    -u $elod_opts.u 2> ${out_elod}   ## stderr and stdout switched for some reason...
+#else
+    -o swiftlink.out
+    && linkage2allegro '${inp_ped}' '${inp_map}' swiftlink -l swiftlink.out
+    && mv linkage.allegro_lod '${out_fparam}'
+#end if
+
+    ]]>
+    </command>
+
+    <inputs>
+        <param name="inp_ped" type="data" format="linkage_pedin" label="Pedigree" />
+        <param name="inp_dat" type="data" format="linkage_recomb" label="Recombination Freqs." />
+        <param name="inp_map" type="data" format="linkage_map" label="Marker Positions" />
+
+        <conditional name="elod_opts" >
+            <param argument="-e" type="select" label="Calculate Expected LOD scores from pedigree only.">
+                <option value="yes">Yes</option>
+                <option value="no" selected="true">No</option>
+            </param>
+            <when value="yes" >
+                <param name="f" argument="-f" type="float" min="0" max="0.99" value="0.0001" label="Frequency" />
+                <param name="w" argument="-w" type="float" min="0" max="1" value="0.5" label="Seperation" />
+                <param name="k" argument="-k" type="text" value="0.00,0.00,1.00" label="Penetrance List" />
+                <param name="u" argument="-u" type="integer" min="1" value="1000000" label="Replicates" />
+            </when>
+            <when value="no" ></when>
+        </conditional>
+
+        <section name="mcmc" title="Marko Chain Monte Carlo (MCMC) Options" expanded="false" >
+            <param argument="-i" type="integer" min="1" value="50000" label="Iterations" />
+            <param argument="-b" type="integer" min="1" value="50000" label="Burn-ins" />
+            <param argument="-s" type="integer" min="1" value="1000" label="Sequential Imputation" />
+            <param argument="-x" type="integer" min="1" value="10" label="Scoring Period" />
+            <param argument="-n" type="integer" min="1" value="5" label="Lod Scores" />
+            <param argument="-R" type="integer" min="1" value="1" label="Runs" />
+            <param argument="-l" type="float" min="0" max="1" value="0.5" label="L-Sampler Probability" />
+        </section>
+
+        <section name="misc" title="Miscellaneous" expanded="true" >
+            <param argument="-X" type="boolean" truevalue="-X" falsevalue="" value="false" label="X-linked"/>
+            <param argument="-a" type="boolean" truevalue="-a" falsevalue="" value="false" label="Affecteds only"/>
+            <param argument="-q" type="integer" min="1" value="1000000" label="Peel-sequence Iterator"/>
+            <param argument="-r" type="data" format="txt" label="Random seeds (single-column)" optional="true" />
+        </section>
+    </inputs>
+
+    <outputs>
+        <data name="out_fparam" format="allegro_fparam" label="${tool.name} on ${on_string}: MPT Linkage File" >
+            <filter>elod_opts['e'] == "no"</filter>
+        </data>
+        <data name="out_elod" format="txt" label="${tool.name} on ${on_string}: Elod score" >
+            <filter>elod_opts['e'] == "yes"</filter>
+        </data>
+    </outputs>
+
+    <tests>
+        <test>
+            <expand macro="test_inputs" />
+
+            <param name="b" value="1000" />
+            <param name="i" value="2000" />
+            <param name="x" value="150" />
+            <param name="e" value="yes" />
+            <param name="u" value="1000" />
+
+            <output name="out_elod" >
+                <assert_contents>
+                    <has_text_matching expression='sex-linked = false' />
+                    <has_text_matching expression='Total\s+\|\s+\d+\.\d+\s*' />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <expand macro="test_inputs" />
+
+            <param name="b" value="5000" />
+            <param name="i" value="100" />
+            <param name="x" value="100" />
+
+            <output name="out_fparam" >
+                <assert_contents>
+                    <has_text_matching expression="(\s+-?\d+\.\d+){4}\s+rs468601" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+SwiftLink performs multipoint parametric linkage analysis on large consanguineous pedigrees and is primarily targeted at pedigrees that cannot be analysed by a Lander-Green algorithm based program, i.e. many markers, but larger pedigrees. The current version of SwiftLink only supports SNP markers.
+    </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/bts704</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 0802a40af216 test-data/datain.21
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/datain.21	Sat Dec 09 17:37:03 2017 -0500
@@ -0,0 +1,1172 @@
+582 0 0 5
+ 0 0.0 0.0 0 
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582
+1  2 	# TRAIT
+ 0.9999 0.0001
+ 1
+ 0.000 0.000 1.000
+3  2 	# rs1296971
+ 0.4583 0.5417
+3  2 	# rs468601
+ 0.1356 0.8644
+3  2 	# rs2821973
+ 0.4083 0.5917
+3  2 	# rs1929150
+ 0.3559 0.6441
+3  2 	# rs2822124
+ 0.4407 0.5593
+3  2 	# rs2775054
+ 0.2583 0.7417
+3  2 	# rs7276618
+ 0.4167 0.5833
+3  2 	# rs392812
+ 0.1000 0.9000
+3  2 	# rs2822368
+ 0.2833 0.7167
+3  2 	# rs6516610
+ 0.3167 0.6833
+3  2 	# rs447455
+ 0.2000 0.8000
+3  2 	# rs437521
+ 0.1667 0.8333
+3  2 	# rs2822554
+ 0.1417 0.8583
+3  2 	# rs2822572
+ 0.1000 0.9000
+3  2 	# rs13050350
+ 0.3167 0.6833
+3  2 	# rs2142236
+ 0.0667 0.9333
+3  2 	# rs2822677
+ 0.0508 0.9492
+3  2 	# rs2822696
+ 0.0833 0.9167
+3  2 	# rs376635
+ 0.4500 0.5500
+3  2 	# rs2822765
+ 0.4333 0.5667
+3  2 	# rs2822780
+ 0.1667 0.8333
+3  2 	# rs465340
+ 0.4917 0.5083
+3  2 	# rs1888398
+ 0.2250 0.7750
+3  2 	# rs458052
+ 0.3333 0.6667
+3  2 	# rs2822907
+ 0.3250 0.6750
+3  2 	# rs8129531
+ 0.2333 0.7667
+3  2 	# rs12053660
+ 0.1500 0.8500
+3  2 	# rs1883003
+ 0.2750 0.7250
+3  2 	# rs2822974
+ 0.4833 0.5167
+3  2 	# rs11088231
+ 0.1667 0.8333
+3  2 	# rs2205239
+ 0.4250 0.5750
+3  2 	# rs2823045
+ 0.2417 0.7583
+3  2 	# rs926164
+ 0.2750 0.7250
+3  2 	# rs2823139
+ 0.2417 0.7583
+3  2 	# rs2823161
+ 0.3667 0.6333
+3  2 	# rs2823194
+ 0.0750 0.9250
+3  2 	# rs2049882
+ 0.0917 0.9083
+3  2 	# rs1736148
+ 0.4417 0.5583
+3  2 	# rs2823301
+ 0.2583 0.7417
+3  2 	# rs6517467
+ 0.2333 0.7667
+3  2 	# rs2064051
+ 0.2333 0.7667
+3  2 	# rs9974915
+ 0.1000 0.9000
+3  2 	# rs2823400
+ 0.3583 0.6417
+3  2 	# rs726634
+ 0.3167 0.6833
+3  2 	# rs7283707
+ 0.1083 0.8917
+3  2 	# rs7283161
+ 0.4333 0.5667
+3  2 	# rs9982633
+ 0.2500 0.7500
+3  2 	# rs2823621
+ 0.4333 0.5667
+3  2 	# rs2051347
+ 0.3000 0.7000
+3  2 	# rs2823702
+ 0.3417 0.6583
+3  2 	# rs189457
+ 0.3167 0.6833
+3  2 	# rs2823748
+ 0.3167 0.6833
+3  2 	# rs2849869
+ 0.2417 0.7583
+3  2 	# rs1667568
+ 0.0917 0.9083
+3  2 	# rs171267
+ 0.4417 0.5583
+3  2 	# rs11911987
+ 0.0333 0.9667
+3  2 	# rs2823881
+ 0.0417 0.9583
+3  2 	# rs2823912
+ 0.0917 0.9083
+3  2 	# rs2032287
+ 0.3333 0.6667
+3  2 	# rs4818278
+ 0.2667 0.7333
+3  2 	# rs11700643
+ 0.2833 0.7167
+3  2 	# rs418989
+ 0.1333 0.8667
+3  2 	# rs4818307
+ 0.0583 0.9417
+3  2 	# rs11701390
+ 0.3667 0.6333
+3  2 	# rs2824192
+ 0.4825 0.5175
+3  2 	# rs2824231
+ 0.4250 0.5750
+3  2 	# rs1501813
+ 0.1917 0.8083
+3  2 	# rs2824273
+ 0.3833 0.6167
+3  2 	# rs2824282
+ 0.3500 0.6500
+3  2 	# rs4536738
+ 0.3000 0.7000
+3  2 	# rs2824292
+ 0.4917 0.5083
+3  2 	# rs208885
+ 0.2250 0.7750
+3  2 	# rs2849886
+ 0.1667 0.8333
+3  2 	# rs764657
+ 0.3917 0.6083
+3  2 	# rs9977638
+ 0.3417 0.6583
+3  2 	# rs2824435
+ 0.2000 0.8000
+3  2 	# rs243570
+ 0.2750 0.7250
+3  2 	# rs243587
+ 0.4917 0.5083
+3  2 	# rs243619
+ 0.4667 0.5333
+3  2 	# rs2824560
+ 0.3333 0.6667
+3  2 	# rs200801
+ 0.5000 0.5000
+3  2 	# rs157740
+ 0.3750 0.6250
+3  2 	# rs2260211
+ 0.1750 0.8250
+3  2 	# rs1491781
+ 0.3750 0.6250
+3  2 	# rs2824646
+ 0.2667 0.7333
+3  2 	# rs2824669
+ 0.3333 0.6667
+3  2 	# rs2824688
+ 0.1417 0.8583
+3  2 	# rs2824699
+ 0.0583 0.9417
+3  2 	# rs2824704
+ 0.3750 0.6250
+3  2 	# rs9983595
+ 0.1750 0.8250
+3  2 	# rs7283555
+ 0.1333 0.8667
+3  2 	# rs2824733
+ 0.2250 0.7750
+3  2 	# rs2824760
+ 0.4167 0.5833
+3  2 	# rs17781453
+ 0.2203 0.7797
+3  2 	# rs978421
+ 0.4583 0.5417
+3  2 	# rs2251831
+ 0.1167 0.8833
+3  2 	# rs1735766
+ 0.3833 0.6167
+3  2 	# rs2824909
+ 0.3667 0.6333
+3  2 	# rs8133676
+ 0.3083 0.6917
+3  2 	# rs8129581
+ 0.0417 0.9583
+3  2 	# rs1159082
+ 0.2083 0.7917
+3  2 	# rs432177
+ 0.2917 0.7083
+3  2 	# rs443581
+ 0.1500 0.8500
+3  2 	# rs2178993
+ 0.4000 0.6000
+3  2 	# rs2825304
+ 0.3917 0.6083
+3  2 	# rs764063
+ 0.4667 0.5333
+3  2 	# rs2825410
+ 0.3917 0.6083
+3  2 	# rs856168
+ 0.2083 0.7917
+3  2 	# rs2825547
+ 0.1167 0.8833
+3  2 	# rs1489734
+ 0.4417 0.5583
+3  2 	# rs434435
+ 0.1583 0.8417
+3  2 	# rs2244367
+ 0.2333 0.7667
+3  2 	# rs2825673
+ 0.1356 0.8644
+3  2 	# rs7277498
+ 0.2917 0.7083
+3  2 	# rs2825728
+ 0.1917 0.8083
+3  2 	# rs2825750
+ 0.0917 0.9083
+3  2 	# rs13433388
+ 0.1167 0.8833
+3  2 	# rs7275645
+ 0.1583 0.8417
+3  2 	# rs2825924
+ 0.3167 0.6833
+3  2 	# rs2825960
+ 0.3250 0.6750
+3  2 	# rs2825977
+ 0.1417 0.8583
+3  2 	# rs2826065
+ 0.4583 0.5417
+3  2 	# rs2826125
+ 0.4083 0.5917
+3  2 	# rs2246644
+ 0.2250 0.7750
+3  2 	# rs2091991
+ 0.2583 0.7417
+3  2 	# rs994455
+ 0.3250 0.6750
+3  2 	# rs2826262
+ 0.1000 0.9000
+3  2 	# rs2826339
+ 0.2833 0.7167
+3  2 	# rs1893329
+ 0.1833 0.8167
+3  2 	# rs2826388
+ 0.4083 0.5917
+3  2 	# rs1351599
+ 0.3250 0.6750
+3  2 	# rs229448
+ 0.3917 0.6083
+3  2 	# rs2826418
+ 0.1417 0.8583
+3  2 	# rs9974471
+ 0.0750 0.9250
+3  2 	# rs2826538
+ 0.2583 0.7417
+3  2 	# rs9981937
+ 0.4500 0.5500
+3  2 	# rs2826596
+ 0.1917 0.8083
+3  2 	# rs6518018
+ 0.4500 0.5500
+3  2 	# rs8126872
+ 0.0583 0.9417
+3  2 	# rs1980966
+ 0.2083 0.7917
+3  2 	# rs2826662
+ 0.4250 0.5750
+3  2 	# rs2826676
+ 0.3000 0.7000
+3  2 	# rs2826713
+ 0.4333 0.5667
+3  2 	# rs1373484
+ 0.2250 0.7750
+3  2 	# rs2826844
+ 0.1500 0.8500
+3  2 	# rs233803
+ 0.0750 0.9250
+3  2 	# rs8134226
+ 0.2500 0.7500
+3  2 	# rs1735990
+ 0.4167 0.5833
+3  2 	# rs2826982
+ 0.3417 0.6583
+3  2 	# rs2827045
+ 0.1083 0.8917
+3  2 	# rs2827102
+ 0.1167 0.8833
+3  2 	# rs2246589
+ 0.2417 0.7583
+3  2 	# rs2154723
+ 0.4667 0.5333
+3  2 	# rs2827203
+ 0.3333 0.6667
+3  2 	# rs2827251
+ 0.0833 0.9167
+3  2 	# rs2827308
+ 0.4583 0.5417
+3  2 	# rs2827322
+ 0.0917 0.9083
+3  2 	# rs2827338
+ 0.3167 0.6833
+3  2 	# rs2014609
+ 0.3000 0.7000
+3  2 	# rs2827606
+ 0.2750 0.7250
+3  2 	# rs2827641
+ 0.2500 0.7500
+3  2 	# rs8127947
+ 0.1250 0.8750
+3  2 	# rs117674
+ 0.3083 0.6917
+3  2 	# rs198114
+ 0.4000 0.6000
+3  2 	# rs405227
+ 0.4083 0.5917
+3  2 	# rs2827880
+ 0.1083 0.8917
+3  2 	# rs8134936
+ 0.0667 0.9333
+3  2 	# rs2828019
+ 0.1667 0.8333
+3  2 	# rs2828068
+ 0.3583 0.6417
+3  2 	# rs2828098
+ 0.4000 0.6000
+3  2 	# rs9980706
+ 0.2333 0.7667
+3  2 	# rs2828167
+ 0.2333 0.7667
+3  2 	# rs2212575
+ 0.3417 0.6583
+3  2 	# rs1514417
+ 0.1917 0.8083
+3  2 	# rs1514414
+ 0.4917 0.5083
+3  2 	# rs2828457
+ 0.1583 0.8417
+3  2 	# rs2828520
+ 0.3417 0.6583
+3  2 	# rs2828549
+ 0.0667 0.9333
+3  2 	# rs2828622
+ 0.2083 0.7917
+3  2 	# rs9977556
+ 0.2000 0.8000
+3  2 	# rs2154734
+ 0.3500 0.6500
+3  2 	# rs1910670
+ 0.2667 0.7333
+3  2 	# rs11087904
+ 0.0917 0.9083
+3  2 	# rs12627150
+ 0.2917 0.7083
+3  2 	# rs2828914
+ 0.1417 0.8583
+3  2 	# rs2829026
+ 0.2667 0.7333
+3  2 	# rs2829049
+ 0.4333 0.5667
+3  2 	# rs2829086
+ 0.3000 0.7000
+3  2 	# rs12053689
+ 0.0167 0.9833
+3  2 	# rs728067
+ 0.3833 0.6167
+3  2 	# rs4816976
+ 0.4083 0.5917
+3  2 	# rs2829227
+ 0.1833 0.8167
+3  2 	# rs17000204
+ 0.0833 0.9167
+3  2 	# rs2829285
+ 0.4167 0.5833
+3  2 	# rs17000332
+ 0.0917 0.9083
+3  2 	# rs17689314
+ 0.0750 0.9250
+3  2 	# rs4283495
+ 0.2083 0.7917
+3  2 	# rs2154526
+ 0.4250 0.5750
+3  2 	# rs2829558
+ 0.3500 0.6500
+3  2 	# rs12626495
+ 0.1667 0.8333
+3  2 	# rs2829726
+ 0.1750 0.8250
+3  2 	# rs2829775
+ 0.0750 0.9250
+3  2 	# rs2829856
+ 0.2833 0.7167
+3  2 	# rs2829914
+ 0.0417 0.9583
+3  2 	# rs2829964
+ 0.4667 0.5333
+3  2 	# rs1787438
+ 0.1083 0.8917
+3  2 	# rs9305268
+ 0.1917 0.8083
+3  2 	# rs3991
+ 0.3000 0.7000
+3  2 	# rs466609
+ 0.1167 0.8833
+3  2 	# rs457581
+ 0.2542 0.7458
+3  2 	# rs468476
+ 0.3250 0.6750
+3  2 	# rs2117454
+ 0.1833 0.8167
+3  2 	# rs219712
+ 0.1083 0.8917
+3  2 	# rs2830206
+ 0.4417 0.5583
+3  2 	# rs2830217
+ 0.0583 0.9417
+3  2 	# rs2830227
+ 0.4417 0.5583
+3  2 	# rs219672
+ 0.4083 0.5917
+3  2 	# rs222920
+ 0.1917 0.8083
+3  2 	# rs222956
+ 0.2417 0.7583
+3  2 	# rs458076
+ 0.4000 0.6000
+3  2 	# rs9967959
+ 0.1667 0.8333
+3  2 	# rs2830442
+ 0.3000 0.7000
+3  2 	# rs2830511
+ 0.2333 0.7667
+3  2 	# rs370850
+ 0.2500 0.7500
+3  2 	# rs229100
+ 0.1333 0.8667
+3  2 	# rs2830585
+ 0.2500 0.7500
+3  2 	# rs2830605
+ 0.3333 0.6667
+3  2 	# rs2830640
+ 0.3833 0.6167
+3  2 	# rs2830715
+ 0.3421 0.6579
+3  2 	# rs969988
+ 0.3644 0.6356
+3  2 	# rs2830768
+ 0.1583 0.8417
+3  2 	# rs235938
+ 0.4333 0.5667
+3  2 	# rs2830801
+ 0.1167 0.8833
+3  2 	# rs2830824
+ 0.0417 0.9583
+3  2 	# rs1452084
+ 0.1250 0.8750
+3  2 	# rs239595
+ 0.1083 0.8917
+3  2 	# rs1376928
+ 0.3917 0.6083
+3  2 	# rs2830933
+ 0.1583 0.8417
+3  2 	# rs456874
+ 0.3750 0.6250
+3  2 	# rs4817181
+ 0.4500 0.5500
+3  2 	# rs2831005
+ 0.2750 0.7250
+3  2 	# rs2409209
+ 0.3136 0.6864
+3  2 	# rs3844464
+ 0.1833 0.8167
+3  2 	# rs9789838
+ 0.2000 0.8000
+3  2 	# rs11088049
+ 0.3250 0.6750
+3  2 	# rs9978929
+ 0.2000 0.8000
+3  2 	# rs2831507
+ 0.3250 0.6750
+3  2 	# rs7278583
+ 0.3333 0.6667
+3  2 	# rs2143682
+ 0.4750 0.5250
+3  2 	# rs1738121
+ 0.0917 0.9083
+3  2 	# rs2831806
+ 0.1667 0.8333
+3  2 	# rs2254751
+ 0.2000 0.8000
+3  2 	# rs9983632
+ 0.1333 0.8667
+3  2 	# rs1028990
+ 0.4083 0.5917
+3  2 	# rs981931
+ 0.4583 0.5417
+3  2 	# rs2832093
+ 0.2500 0.7500
+3  2 	# rs2832194
+ 0.4583 0.5417
+3  2 	# rs2300301
+ 0.1000 0.9000
+3  2 	# rs2832373
+ 0.1167 0.8833
+3  2 	# rs363478
+ 0.1917 0.8083
+3  2 	# rs363582
+ 0.1583 0.8417
+3  2 	# rs17772700
+ 0.0500 0.9500
+3  2 	# rs146662
+ 0.4000 0.6000
+3  2 	# rs2832463
+ 0.0667 0.9333
+3  2 	# rs455477
+ 0.1167 0.8833
+3  2 	# rs9976786
+ 0.0667 0.9333
+3  2 	# rs2832547
+ 0.0500 0.9500
+3  2 	# rs16985999
+ 0.0083 0.9917
+3  2 	# rs614118
+ 0.1833 0.8167
+3  2 	# rs2832729
+ 0.2333 0.7667
+3  2 	# rs9636832
+ 0.1833 0.8167
+3  2 	# rs9305434
+ 0.4167 0.5833
+3  2 	# rs2833124
+ 0.3000 0.7000
+3  2 	# rs4817363
+ 0.4000 0.6000
+3  2 	# rs2833160
+ 0.0667 0.9333
+3  2 	# rs2833162
+ 0.1250 0.8750
+3  2 	# rs7280222
+ 0.0500 0.9500
+3  2 	# rs1571691
+ 0.3833 0.6167
+3  2 	# rs2833270
+ 0.1000 0.9000
+3  2 	# rs9305454
+ 0.0833 0.9167
+3  2 	# rs845972
+ 0.3917 0.6083
+3  2 	# rs1034314
+ 0.2917 0.7083
+3  2 	# rs9984499
+ 0.1271 0.8729
+3  2 	# rs2833390
+ 0.1250 0.8750
+3  2 	# rs2833406
+ 0.2667 0.7333
+3  2 	# rs475142
+ 0.1917 0.8083
+3  2 	# rs577738
+ 0.1833 0.8167
+3  2 	# rs2833444
+ 0.3250 0.6750
+3  2 	# rs2409416
+ 0.4333 0.5667
+3  2 	# rs204740
+ 0.1500 0.8500
+3  2 	# rs964603
+ 0.1583 0.8417
+3  2 	# rs2211781
+ 0.3333 0.6667
+3  2 	# rs11700457
+ 0.1333 0.8667
+3  2 	# rs11910494
+ 0.3583 0.6417
+3  2 	# rs2833584
+ 0.0750 0.9250
+3  2 	# rs12165267
+ 0.1500 0.8500
+3  2 	# rs9305486
+ 0.3500 0.6500
+3  2 	# rs1892577
+ 0.4250 0.5750
+3  2 	# rs2833637
+ 0.1000 0.9000
+3  2 	# rs2833654
+ 0.4167 0.5833
+3  2 	# rs876382
+ 0.4583 0.5417
+3  2 	# rs12151995
+ 0.3167 0.6833
+3  2 	# rs2833718
+ 0.1167 0.8833
+3  2 	# rs2833757
+ 0.2167 0.7833
+3  2 	# rs11088218
+ 0.1667 0.8333
+3  2 	# rs2833854
+ 0.1750 0.8250
+3  2 	# rs1892655
+ 0.4333 0.5667
+3  2 	# rs7284048
+ 0.0750 0.9250
+3  2 	# rs845015
+ 0.4750 0.5250
+3  2 	# rs6517109
+ 0.1750 0.8250
+3  2 	# rs2014283
+ 0.3917 0.6083
+3  2 	# rs7278366
+ 0.2500 0.7500
+3  2 	# rs4817514
+ 0.4667 0.5333
+3  2 	# rs762236
+ 0.4167 0.5833
+3  2 	# rs2834076
+ 0.3362 0.6638
+3  2 	# rs6517142
+ 0.2750 0.7250
+3  2 	# rs2834098
+ 0.1917 0.8083
+3  2 	# rs2834101
+ 0.2333 0.7667
+3  2 	# rs9305523
+ 0.1583 0.8417
+3  2 	# rs2834135
+ 0.0833 0.9167
+3  2 	# rs2236758
+ 0.3583 0.6417
+3  2 	# rs2834168
+ 0.2500 0.7500
+3  2 	# rs735299
+ 0.4500 0.5500
+3  2 	# rs9974246
+ 0.3250 0.6750
+3  2 	# rs3761347
+ 0.1333 0.8667
+3  2 	# rs2268247
+ 0.0667 0.9333
+3  2 	# rs9636869
+ 0.1333 0.8667
+3  2 	# rs2073370
+ 0.4667 0.5333
+3  2 	# rs734746
+ 0.3000 0.7000
+3  2 	# rs2186553
+ 0.4417 0.5583
+3  2 	# rs2834371
+ 0.5000 0.5000
+3  2 	# rs873811
+ 0.0417 0.9583
+3  2 	# rs7278204
+ 0.1833 0.8167
+3  2 	# rs2834461
+ 0.4250 0.5750
+3  2 	# rs4817646
+ 0.0833 0.9167
+3  2 	# rs2834473
+ 0.4333 0.5667
+3  2 	# rs1012944
+ 0.3667 0.6333
+3  2 	# rs11700954
+ 0.3220 0.6780
+3  2 	# rs2300387
+ 0.3051 0.6949
+3  2 	# rs9305556
+ 0.4068 0.5932
+3  2 	# rs2834609
+ 0.3167 0.6833
+3  2 	# rs7282726
+ 0.3583 0.6417
+3  2 	# rs2243988
+ 0.3390 0.6610
+3  2 	# rs2268288
+ 0.2250 0.7750
+3  2 	# rs2284617
+ 0.2000 0.8000
+3  2 	# rs8134179
+ 0.1583 0.8417
+3  2 	# rs9984470
+ 0.0583 0.9417
+3  2 	# rs2834706
+ 0.3667 0.6333
+3  2 	# rs2834714
+ 0.3667 0.6333
+3  2 	# rs2834729
+ 0.1333 0.8667
+3  2 	# rs881386
+ 0.3667 0.6333
+3  2 	# rs7277157
+ 0.2167 0.7833
+3  2 	# rs984659
+ 0.4833 0.5167
+3  2 	# rs12626430
+ 0.3917 0.6083
+3  2 	# rs2075902
+ 0.3000 0.7000
+3  2 	# rs2834843
+ 0.2417 0.7583
+3  2 	# rs11088316
+ 0.2583 0.7417
+3  2 	# rs2834909
+ 0.4833 0.5167
+3  2 	# rs1882766
+ 0.2583 0.7417
+3  2 	# rs2834939
+ 0.3417 0.6583
+3  2 	# rs2205112
+ 0.4417 0.5583
+3  2 	# rs1627997
+ 0.2583 0.7417
+3  2 	# rs2835076
+ 0.1750 0.8250
+3  2 	# rs2242793
+ 0.1833 0.8167
+3  2 	# rs2835165
+ 0.4917 0.5083
+3  2 	# rs735143
+ 0.2667 0.7333
+3  2 	# rs2252991
+ 0.3250 0.6750
+3  2 	# rs2070515
+ 0.4917 0.5083
+3  2 	# rs7354757
+ 0.3167 0.6833
+3  2 	# rs2835346
+ 0.3250 0.6750
+3  2 	# rs219757
+ 0.3083 0.6917
+3  2 	# rs2000546
+ 0.3917 0.6083
+3  2 	# rs9976609
+ 0.1417 0.8583
+3  2 	# rs7281079
+ 0.1333 0.8667
+3  2 	# rs2835424
+ 0.4583 0.5417
+3  2 	# rs2409840
+ 0.4500 0.5500
+3  2 	# rs2835449
+ 0.3167 0.6833
+3  2 	# rs2073416
+ 0.1500 0.8500
+3  2 	# rs2845804
+ 0.3814 0.6186
+3  2 	# rs2016223
+ 0.2667 0.7333
+3  2 	# rs8134293
+ 0.2833 0.7167
+3  2 	# rs2073425
+ 0.3793 0.6207
+3  2 	# rs2835561
+ 0.2750 0.7250
+3  2 	# rs2249947
+ 0.4583 0.5417
+3  2 	# rs2835695
+ 0.3500 0.6500
+3  2 	# rs8131184
+ 0.4750 0.5250
+3  2 	# rs2835808
+ 0.3083 0.6917
+3  2 	# rs928723
+ 0.4333 0.5667
+3  2 	# rs3392
+ 0.3500 0.6500
+3  2 	# rs857958
+ 0.2083 0.7917
+3  2 	# rs2835955
+ 0.3898 0.6102
+3  2 	# rs3787840
+ 0.1750 0.8250
+3  2 	# rs4816585
+ 0.4083 0.5917
+3  2 	# rs2836034
+ 0.0500 0.9500
+3  2 	# rs9976411
+ 0.1417 0.8583
+3  2 	# rs2836067
+ 0.2917 0.7083
+3  2 	# rs2836096
+ 0.3167 0.6833
+3  2 	# rs2836143
+ 0.4492 0.5508
+3  2 	# rs2836278
+ 0.2583 0.7417
+3  2 	# rs2836316
+ 0.2333 0.7667
+3  2 	# rs2836338
+ 0.4833 0.5167
+3  2 	# rs2836344
+ 0.3417 0.6583
+3  2 	# rs2836379
+ 0.1000 0.9000
+3  2 	# rs2836400
+ 0.4583 0.5417
+3  2 	# rs9978004
+ 0.0917 0.9083
+3  2 	# rs2836478
+ 0.1750 0.8250
+3  2 	# rs2836526
+ 0.1441 0.8559
+3  2 	# rs2836544
+ 0.2917 0.7083
+3  2 	# rs1475878
+ 0.2667 0.7333
+3  2 	# rs2836640
+ 0.4250 0.5750
+3  2 	# rs2836656
+ 0.4667 0.5333
+3  2 	# rs2836664
+ 0.4583 0.5417
+3  2 	# rs2070531
+ 0.4250 0.5750
+3  2 	# rs12626608
+ 0.0917 0.9083
+3  2 	# rs2836754
+ 0.3667 0.6333
+3  2 	# rs13052608
+ 0.3500 0.6500
+3  2 	# rs733623
+ 0.1333 0.8667
+3  2 	# rs8130738
+ 0.3083 0.6917
+3  2 	# rs4816610
+ 0.4917 0.5083
+3  2 	# rs404074
+ 0.1417 0.8583
+3  2 	# rs2836891
+ 0.2500 0.7500
+3  2 	# rs7281463
+ 0.4407 0.5593
+3  2 	# rs2837011
+ 0.2167 0.7833
+3  2 	# rs517871
+ 0.2917 0.7083
+3  2 	# rs512384
+ 0.3917 0.6083
+3  2 	# rs10854398
+ 0.4083 0.5917
+3  2 	# rs2239385
+ 0.2167 0.7833
+3  2 	# rs12483089
+ 0.4250 0.5750
+3  2 	# rs11088492
+ 0.1500 0.8500
+3  2 	# rs467109
+ 0.2000 0.8000
+3  2 	# rs2837132
+ 0.2833 0.7167
+3  2 	# rs4816642
+ 0.2083 0.7917
+3  2 	# rs388152
+ 0.1250 0.8750
+3  2 	# rs438591
+ 0.3333 0.6667
+3  2 	# rs12106362
+ 0.0917 0.9083
+3  2 	# rs3819595
+ 0.1417 0.8583
+3  2 	# rs2299787
+ 0.0667 0.9333
+3  2 	# rs4816665
+ 0.1667 0.8333
+3  2 	# rs2837343
+ 0.4583 0.5417
+3  2 	# rs760168
+ 0.3750 0.6250
+3  2 	# rs2996053
+ 0.2500 0.7500
+3  2 	# rs2837382
+ 0.2583 0.7417
+3  2 	# rs2837426
+ 0.1583 0.8417
+3  2 	# rs8132673
+ 0.2167 0.7833
+3  2 	# rs7278658
+ 0.2750 0.7250
+3  2 	# rs2837480
+ 0.3500 0.6500
+3  2 	# rs2837508
+ 0.4500 0.5500
+3  2 	# rs1882760
+ 0.4500 0.5500
+3  2 	# rs2837574
+ 0.4333 0.5667
+3  2 	# rs1882756
+ 0.3559 0.6441
+3  2 	# rs9985057
+ 0.4746 0.5254
+3  2 	# rs12481965
+ 0.1167 0.8833
+3  2 	# rs2837699
+ 0.3833 0.6167
+3  2 	# rs9977890
+ 0.3667 0.6333
+3  2 	# rs2837765
+ 0.2167 0.7833
+3  2 	# rs2837770
+ 0.4083 0.5917
+3  2 	# rs8132311
+ 0.2833 0.7167
+3  2 	# rs2837798
+ 0.1583 0.8417
+3  2 	# rs7283279
+ 0.2417 0.7583
+3  2 	# rs2837854
+ 0.2333 0.7667
+3  2 	# rs732994
+ 0.4333 0.5667
+3  2 	# rs2837864
+ 0.4333 0.5667
+3  2 	# rs9636977
+ 0.4667 0.5333
+3  2 	# rs2837887
+ 0.4417 0.5583
+3  2 	# rs9305716
+ 0.3898 0.6102
+3  2 	# rs9981541
+ 0.4083 0.5917
+3  2 	# rs2094877
+ 0.2833 0.7167
+3  2 	# rs2837959
+ 0.2417 0.7583
+3  2 	# rs2837960
+ 0.1000 0.9000
+3  2 	# rs4816713
+ 0.2083 0.7917
+3  2 	# rs2837970
+ 0.3917 0.6083
+3  2 	# rs1541103
+ 0.4000 0.6000
+3  2 	# rs2410416
+ 0.3167 0.6833
+3  2 	# rs441810
+ 0.1750 0.8250
+3  2 	# rs390789
+ 0.3729 0.6271
+3  2 	# rs2838032
+ 0.0750 0.9250
+3  2 	# rs9979006
+ 0.0917 0.9083
+3  2 	# rs468440
+ 0.3583 0.6417
+3  2 	# rs2298857
+ 0.2000 0.8000
+3  2 	# rs3761373
+ 0.0917 0.9083
+3  2 	# rs9975623
+ 0.2917 0.7083
+3  2 	# rs2838067
+ 0.2500 0.7500
+3  2 	# rs2838070
+ 0.3250 0.6750
+3  2 	# rs2838077
+ 0.3917 0.6083
+3  2 	# rs2247788
+ 0.1583 0.8417
+3  2 	# rs9984259
+ 0.2373 0.7627
+3  2 	# rs7279061
+ 0.1833 0.8167
+3  2 	# rs2838090
+ 0.2583 0.7417
+3  2 	# rs8126725
+ 0.0583 0.9417
+3  2 	# rs12483161
+ 0.4417 0.5583
+3  2 	# rs2838121
+ 0.2000 0.8000
+3  2 	# rs2277793
+ 0.2833 0.7167
+3  2 	# rs2236440
+ 0.1500 0.8500
+3  2 	# rs2277795
+ 0.1083 0.8917
+3  2 	# rs365163
+ 0.3750 0.6250
+3  2 	# rs7280126
+ 0.3250 0.6750
+3  2 	# rs8133606
+ 0.2500 0.7500
+3  2 	# rs11701751
+ 0.1833 0.8167
+3  2 	# rs7275759
+ 0.0583 0.9417
+3  2 	# rs220229
+ 0.1667 0.8333
+3  2 	# rs220245
+ 0.1583 0.8417
+3  2 	# rs150796
+ 0.1500 0.8500
+3  2 	# rs2839461
+ 0.1333 0.8667
+3  2 	# rs220109
+ 0.4583 0.5417
+3  2 	# rs13051533
+ 0.4661 0.5339
+3  2 	# rs1563357
+ 0.1250 0.8750
+3  2 	# rs4148105
+ 0.4000 0.6000
+3  2 	# rs7281345
+ 0.1583 0.8417
+3  2 	# rs7275482
+ 0.1750 0.8250
+3  2 	# rs2236705
+ 0.1167 0.8833
+3  2 	# rs11701981
+ 0.2250 0.7750
+3  2 	# rs755946
+ 0.4500 0.5500
+3  2 	# rs3814900
+ 0.0750 0.9250
+3  2 	# rs9784215
+ 0.3500 0.6500
+3  2 	# rs8130358
+ 0.2417 0.7583
+3  2 	# rs2839536
+ 0.4333 0.5667
+3  2 	# rs228082
+ 0.4750 0.5250
+3  2 	# rs11701162
+ 0.3083 0.6917
+3  2 	# rs380422
+ 0.2288 0.7712
+3  2 	# rs2138327
+ 0.3000 0.7000
+3  2 	# rs2839576
+ 0.3333 0.6667
+3  2 	# rs7279886
+ 0.3000 0.7000
+3  2 	# rs2839585
+ 0.2417 0.7583
+3  2 	# rs1672133
+ 0.1417 0.8583
+3  2 	# rs2027745
+ 0.2712 0.7288
+3  2 	# rs879648
+ 0.2500 0.7500
+3  2 	# rs2839641
+ 0.4000 0.6000
+3  2 	# rs762391
+ 0.2333 0.7667
+3  2 	# rs638268
+ 0.1417 0.8583
+3  2 	# rs566038
+ 0.0667 0.9333
+3  2 	# rs681210
+ 0.2917 0.7083
+3  2 	# rs672163
+ 0.1167 0.8833
+3  2 	# rs657918
+ 0.2250 0.7750
+3  2 	# rs162382
+ 0.3390 0.6610
+3  2 	# rs1107204
+ 0.4083 0.5917
+3  2 	# rs4819314
+ 0.0750 0.9250
+3  2 	# rs2838429
+ 0.3500 0.6500
+3  2 	# rs3737358
+ 0.0750 0.9250
+3  2 	# rs2277806
+ 0.2333 0.7667
+3  2 	# rs743479
+ 0.4909 0.5091
+3  2 	# rs2070561
+ 0.2583 0.7417
+3  2 	# rs2018054
+ 0.3083 0.6917
+3  2 	# rs2256817
+ 0.4083 0.5917
+3  2 	# rs2070572
+ 0.4237 0.5763
+3  2 	# rs2838551
+ 0.3667 0.6333
+3  2 	# rs2003775
+ 0.2500 0.7500
+3  2 	# rs2838567
+ 0.1917 0.8083
+3  2 	# rs8134902
+ 0.3417 0.6583
+3  2 	# rs11702525
+ 0.2333 0.7667
+3  2 	# rs13051885
+ 0.4250 0.5750
+3  2 	# rs1107121
+ 0.3667 0.6333
+3  2 	# rs235380
+ 0.1333 0.8667
+3  2 	# rs2838674
+ 0.3250 0.6750
+3  2 	# rs2838704
+ 0.3833 0.6167
+3  2 	# rs3788142
+ 0.2250 0.7750
+3  2 	# rs760462
+ 0.2417 0.7583
+3  2 	# rs3788151
+ 0.1000 0.9000
+3  2 	# rs2838738
+ 0.4750 0.5250
+3  2 	# rs7283236
+ 0.3833 0.6167
+3  2 	# rs2838753
+ 0.2833 0.7167
+3  2 	# rs2838760
+ 0.3000 0.7000
+3  2 	# rs2838763
+ 0.3000 0.7000
+3  2 	# rs7281416
+ 0.3475 0.6525
+3  2 	# rs10098
+ 0.4417 0.5583
+3  2 	# rs914237
+ 0.0750 0.9250
+3  2 	# rs2838880
+ 0.4333 0.5667
+3  2 	# rs9306125
+ 0.2917 0.7083
+3  2 	# rs2026886
+ 0.3833 0.6167
+3  2 	# rs2838922
+ 0.1167 0.8833
+3  2 	# rs2236461
+ 0.1833 0.8167
+3  2 	# rs2838950
+ 0.2583 0.7417
+3  2 	# rs2838961
+ 0.3500 0.6500
+3  2 	# rs2838965
+ 0.4333 0.5667
+3  2 	# rs1556335
+ 0.3500 0.6500
+3  2 	# rs2776402
+ 0.2417 0.7583
+3  2 	# rs4819179
+ 0.2917 0.7083
+3  2 	# rs2839094
+ 0.3583 0.6417
+3  2 	# rs2156430
+ 0.3644 0.6356
+3  2 	# rs8133866
+ 0.2750 0.7250
+3  2 	# rs2839260
+ 0.2250 0.7750
+3  2 	# rs6518304
+ 0.3051 0.6949
+ 0 0
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+ 1      2.0  1.0
diff -r 000000000000 -r 0802a40af216 test-data/map.21
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/map.21	Sat Dec 09 17:37:03 2017 -0500
@@ -0,0 +1,582 @@
+#Chr     Genpos       Marker     Physpos    Nr
+ 21    0.70496629   rs1296971   13609442     1
+ 21    0.77494263    rs468601   13769165     2
+ 21    0.85010932   rs2821973   13899316     3
+ 21    1.01291458   rs1929150   14051249     4
+ 21    1.07552959   rs2822124   14088675     5
+ 21    1.16577144   rs2775054   14121682     6
+ 21    1.34457997   rs7276618   14197852     7
+ 21    1.44169062    rs392812   14252347     8
+ 21    1.60661592   rs2822368   14311592     9
+ 21    1.73090413   rs6516610   14385827    10
+ 21    1.78470487    rs447455   14502698    11
+ 21    1.89865013    rs437521   14513560    12
+ 21    1.95928889   rs2822554   14585162    13
+ 21    2.00968909   rs2822572   14618073    14
+ 21    2.09569547  rs13050350   14653413    15
+ 21    2.14611500   rs2142236   14748155    16
+ 21    2.30459845   rs2822677   14767432    17
+ 21    2.35507107   rs2822696   14783326    18
+ 21    2.49458320    rs376635   14788185    19
+ 21    2.54981913   rs2822765   14843387    20
+ 21    2.69205997   rs2822780   14875052    21
+ 21    2.74542953    rs465340   14884525    22
+ 21    2.80926447   rs1888398   14981052    23
+ 21    2.86888387    rs458052   15013563    24
+ 21    2.93942924   rs2822907   15057767    25
+ 21    2.99612354   rs8129531   15061195    26
+ 21    3.15050759  rs12053660   15067326    27
+ 21    3.48398239   rs1883003   15147347    28
+ 21    3.62725156   rs2822974   15185311    29
+ 21    3.69755891  rs11088231   15247441    30
+ 21    3.83233721   rs2205239   15365789    31
+ 21    4.03050303   rs2823045   15382630    32
+ 21    4.11519240    rs926164   15435118    33
+ 21    4.17500340   rs2823139   15498654    34
+ 21    4.22973041   rs2823161   15515055    35
+ 21    4.31848934   rs2823194   15568649    36
+ 21    4.53372425   rs2049882   15633372    37
+ 21    4.62105207   rs1736148   15735083    38
+ 21    4.80636119   rs2823301   15780469    39
+ 21    4.88644465   rs6517467   15806025    40
+ 21    4.96357163   rs2064051   15860950    41
+ 21    5.04209154   rs9974915   15879012    42
+ 21    5.09648993   rs2823400   15922925    43
+ 21    5.28044978    rs726634   15952748    44
+ 21    5.33607360   rs7283707   16048865    45
+ 21    5.52020653   rs7283161   16247081    46
+ 21    5.60568022   rs9982633   16341775    47
+ 21    5.70676016   rs2823621   16453860    48
+ 21    5.81125072   rs2051347   16485140    49
+ 21    5.90261793   rs2823702   16551609    50
+ 21    6.11205825    rs189457   16586547    51
+ 21    6.19207523   rs2823748   16597546    52
+ 21    6.50682420   rs2849869   16651064    53
+ 21    6.65214516   rs1667568   16668191    54
+ 21    6.71981324    rs171267   16678743    55
+ 21    6.82475021  rs11911987   16722383    56
+ 21    7.39610093   rs2823881   16856068    57
+ 21    7.50376261   rs2823912   16917157    58
+ 21    7.63480472   rs2032287   16930320    59
+ 21    7.84039602   rs4818278   16998424    60
+ 21    8.04214302  rs11700643   17038979    61
+ 21    8.22354552    rs418989   17157305    62
+ 21    8.36525000   rs4818307   17217065    63
+ 21    8.45433331  rs11701390   17283040    64
+ 21    8.51634344   rs2824192   17343668    65
+ 21    8.67406372   rs2824231   17392912    66
+ 21    8.77025758   rs1501813   17554542    67
+ 21    8.82932246   rs2824273   17561990    68
+ 21    8.88853994   rs2824282   17645542    69
+ 21    9.03723097   rs4536738   17662409    70
+ 21    9.09085593   rs2824292   17709047    71
+ 21    9.16009205    rs208885   17730794    72
+ 21    9.53979856   rs2849886   17786057    73
+ 21    9.59018991    rs764657   17848524    74
+ 21    9.69271956   rs9977638   17890191    75
+ 21    9.85245414   rs2824435   17966268    76
+ 21   10.08197365    rs243570   18050577    77
+ 21   10.35520368    rs243587   18076288    78
+ 21   10.47428859    rs243619   18133788    79
+ 21   10.53651389   rs2824560   18225088    80
+ 21   10.61943861    rs200801   18255517    81
+ 21   10.67244619    rs157740   18325093    82
+ 21   10.79821762   rs2260211   18346822    83
+ 21   11.00225432   rs1491781   18406009    84
+ 21   11.15996564   rs2824646   18428522    85
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+ 21   11.45964144   rs2824699   18483226    88
+ 21   11.64771978   rs2824704   18490357    89
+ 21   11.76380297   rs9983595   18549169    90
+ 21   11.84781755   rs7283555   18581924    91
+ 21   12.11384302   rs2824733   18610953    92
+ 21   12.17280440   rs2824760   18643999    93
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+ 21   12.38984244    rs978421   18764344    95
+ 21   12.44711692   rs2251831   18789375    96
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+ 21   13.37982622   rs2825410   19494502   107
+ 21   13.59530607    rs856168   19626353   108
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+ 21   13.75352001   rs1489734   19793599   110
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+ 21   13.98574411   rs2825673   19888587   113
+ 21   14.14320618   rs7277498   19951997   114
+ 21   14.20879296   rs2825728   19969339   115
+ 21   14.28647592   rs2825750   19983882   116
+ 21   14.33689830  rs13433388   20069219   117
+ 21   14.38898773   rs7275645   20167678   118
+ 21   14.44017677   rs2825924   20246520   119
+ 21   14.50315223   rs2825960   20320715   120
+ 21   14.56015678   rs2825977   20348756   121
+ 21   14.61166764   rs2826065   20478347   122
+ 21   14.79246064   rs2826125   20571466   123
+ 21   14.90289354   rs2246644   20645886   124
+ 21   15.04596182   rs2091991   20691564   125
+ 21   15.18648966    rs994455   20705648   126
+ 21   15.53559341   rs2826262   20743064   127
+ 21   15.66356127   rs2826339   20806826   128
+ 21   15.77781450   rs1893329   20830425   129
+ 21   15.86446260   rs2826388   20848008   130
+ 21   15.95926952   rs1351599   20913703   131
+ 21   16.05729287    rs229448   20933061   132
+ 21   16.11368606   rs2826418   20949969   133
+ 21   16.47246854   rs9974471   21056224   134
+ 21   16.66392288   rs2826538   21110606   135
+ 21   16.79121263   rs9981937   21134312   136
+ 21   16.85341215   rs2826596   21183086   137
+ 21   17.04571292   rs6518018   21296154   138
+ 21   17.10290055   rs8126872   21345875   139
+ 21   17.18846294   rs1980966   21384976   140
+ 21   17.34205820   rs2826662   21414302   141
+ 21   17.42614487   rs2826676   21427970   142
+ 21   17.51471805   rs2826713   21451562   143
+ 21   17.56528732   rs1373484   21594668   144
+ 21   17.64265500   rs2826844   21743514   145
+ 21   17.85431911    rs233803   21809131   146
+ 21   17.91111695   rs8134226   21864007   147
+ 21   17.96645267   rs1735990   21972669   148
+ 21   18.03585827   rs2826982   22043979   149
+ 21   18.14172180   rs2827045   22094903   150
+ 21   18.20441422   rs2827102   22169091   151
+ 21   18.43775705   rs2246589   22210543   152
+ 21   18.67287429   rs2154723   22258522   153
+ 21   18.85099488   rs2827203   22289388   154
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+ 21   18.99671746   rs2827308   22545897   156
+ 21   19.05774110   rs2827322   22564337   157
+ 21   19.13631789   rs2827338   22576117   158
+ 21   19.20362216   rs2014609   22717064   159
+ 21   19.26613313   rs2827606   22865549   160
+ 21   19.32281282   rs2827641   22917993   161
+ 21   19.52863920   rs8127947   23088645   162
+ 21   19.62941496    rs117674   23181728   163
+ 21   19.69196960    rs198114   23321910   164
+ 21   19.74649998    rs405227   23364298   165
+ 21   19.81984364   rs2827880   23421443   166
+ 21   19.90502305   rs8134936   23558338   167
+ 21   19.95943904   rs2828019   23589727   168
+ 21   20.08961268   rs2828068   23618853   169
+ 21   20.14554663   rs2828098   23674565   170
+ 21   20.23269491   rs9980706   23719145   171
+ 21   20.28980444   rs2828167   23752189   172
+ 21   20.34721944   rs2212575   23858500   173
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+ 21   20.69805264   rs2828457   24015036   176
+ 21   20.74919837   rs2828520   24064990   177
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+ 21   21.00866634   rs2828622   24215779   179
+ 21   21.06311429   rs9977556   24246806   180
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+ 21   21.36223878  rs11087904   24424999   183
+ 21   21.53371556  rs12627150   24432464   184
+ 21   21.69150159   rs2828914   24512033   185
+ 21   21.74270098   rs2829026   24670327   186
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+ 21   21.85804827   rs2829086   24734850   188
+ 21   22.00320719  rs12053689   24836768   189
+ 21   22.08952329    rs728067   24863804   190
+ 21   22.21825129   rs4816976   24889274   191
+ 21   22.26888477   rs2829227   24946353   192
+ 21   22.32072493  rs17000204   24953391   193
+ 21   22.37522446   rs2829285   25002830   194
+ 21   22.55858143  rs17000332   25025907   195
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+ 21   22.83590284   rs2154526   25411108   198
+ 21   22.95961680   rs2829558   25436468   199
+ 21   23.00970055  rs12626495   25531117   200
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+ 21   23.25239439   rs2829914   26100421   204
+ 21   23.30483232   rs2829964   26164267   205
+ 21   23.36264473   rs1787438   26195960   206
+ 21   23.41607023   rs9305268   26261205   207
+ 21   23.51317697      rs3991   26350127   208
+ 21   23.56570795    rs466609   26428188   209
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+ 21   23.73814430   rs2117454   26645152   212
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diff -r 000000000000 -r 0802a40af216 test-data/pedin.21
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pedin.21	Sat Dec 09 17:37:03 2017 -0500
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