# HG changeset patch
# User iuc
# Date 1512819582 18000
# Node ID 8c29e3621475d8f538a4ab2a8a0f6042509b3aa0

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831

diff -r 000000000000 -r 8c29e3621475 allegro.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/allegro.xml	Sat Dec 09 06:39:42 2017 -0500
@@ -0,0 +1,272 @@
+<tool id="allegro" name="Allegro" version="@VER@.0" >
+    <description>Linkage and Haplotype analysis</description>
+    <macros>
+        <token name="@VER@">2</token>
+        <xml name="macro_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="@VER@">allegro</requirement>
+    </requirements>
+    <version_command><![CDATA[
+    allegro 2>&1 | head -1 | awk -F' ' '{print $2}'
+    ]]>
+    </version_command>
+    <command detect_errors='exit_code'>allegro $allegro_conf</command>
+
+    <configfiles>
+        <configfile name="allegro_conf" ><![CDATA[
+PREFILE $inp_ped
+DATFILE $inp_dat
+#if $inp_map
+MAPFILE $inp_map
+#end if
+
+#if $cond_haplotypes.opt_haplotypes == 'yes'
+HAPLOTYPE haplo.out ${out_ihaplo} ${out_founder} inher.out
+        #if $cond_haplotypes.opt_crossover
+CROSSOVERRATE combined.out ${out_combined_cross}
+        #end if
+#elif $cond_haplotypes.opt_haplotypes.value == 'no'
+    #if $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_type.value == 'defaults'
+MODEL $cond_haplotypes.section_linkage.extra_linkage_mptspt.value par ${opt_xlinked} het param.mpt ${out_fparam}
+
+    #elif $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_type.value == 'allele_sharing'
+MODEL $cond_haplotypes.section_linkage.extra_linkage_mptspt.value $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_linexp.value $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_scoring.value $cond_haplotypes.section_linkage.cond_linktype.extra_weighting.value param.mpt ${out_linexp}
+ 
+    #elif $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_type.value == 'classical'
+        #if $cond_haplotypes.section_linkage.cond_linktype.cond_customfreqs.opt_custom_freqs.value == 'yes'
+MODEL $cond_haplotypes.section_linkage.extra_linkage_mptspt.value par $opt_xlinked} freq:$cond_haplotypes.section_linkage.cond_linktype.cond_customfreqs.extra_linkage_par_freq pen:$cond_haplotypes.section_linkage.cond_linktype.cond_customfreqs.extra_linkage_par_pen $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_par_het param.mpt ${out_fparam}
+        #end if
+    #end if
+
+    #if $cond_haplotypes.section_linkage.cond_steps.extra_steps_type.value == 'STEPS'
+STEPS $cond_haplotypes.section_linkage.cond_steps.extra_steps
+    #elif $cond_haplotypes.section_linkage.cond_steps.extra_steps_type.value == 'STEPFILE'
+STEPFILE $cond_haplotypes.section_linkage.cond_steps.inp_stepfile
+    #elif $cond_haplotypes.section_linkage.cond_steps.extra_steps_type.value == 'MAXSTEPLENGTH'
+MAXSTEPLENGTH $cond_haplotypes.section_linkage.cond_steps.extra_maxstep
+    #end if
+#end if
+
+#if $opt_xlinked.value == 'X'
+SEXSPECIFIC on
+#end if
+
+ENTROPY ${opt_entropy}
+NPLEXACTP ${opt_nplexactp}
+
+#if $cond_pairwise.opt_pairwise.value == 'yes'
+PAIRWISEIBD $cond_haplotypes.section_linkage.extra_linkage_mptspt.value $cond_pairwise.extra_pairwise_type.value
+#end if
+
+
+#if $cond_sim.opt_sim.value == 'yes'
+SIMULATE $cond_sim.extra_sim_dloc $cond_sim.extra_sim_npre $cond_sim.extra_sim_rep $cond_sim.extra_sim_err $cond_sim.extra_sim_yield $cond_sim.extra_sim_het
+#end if
+
+MAXMEMORY 102400
+UNIT $opt_unit
+
+UNINFORMATIVE
+
+
+]]>
+        </configfile>
+    </configfiles>
+
+    <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" optional="true" />
+
+        <conditional name="cond_haplotypes" >
+            <param name="opt_haplotypes" type="select" label="Use Haplotypes?" >
+                <option value="yes" >Yes</option>
+                <option value="no" selected="true" >No</option>
+            </param>
+
+            <when value="yes" >
+                <param name="opt_crossover" type="boolean" value="false" label="Show crossover rate" />
+            </when>
+            <when value="no" >
+                <section name="section_linkage" title="Linkage" expanded="true" >
+                    <param name="extra_linkage_mptspt" type="select" label="Use multipoint IBD sharing probabilities, instead of single point" >
+                        <option value="mpt" selected="true" >mpt</option>
+                        <option value="spt" >spt</option>
+                    </param>
+
+                    <conditional name="cond_linktype" >
+                        <param name="extra_linkage_type" type="select" label="Type of analysis" >
+                            <option value="defaults" selected="true" >Defaults</option>
+                            <option value="allele_sharing" >Allele Sharing</option>
+                            <option value="classical" >Classical</option>
+                        </param>
+
+                        <when value="defaults" />
+
+                        <when value="allele_sharing">
+                            <param name="extra_linkage_linexp" type="select" label="Linear or Exponential" >
+                                <option value="lin" >Linear</option>
+                                <option value="exp" >Exponential</option>
+                            </param>
+                            <param name="extra_linkage_scoring" type="select" label="Scoring function" >
+                                <option value="pairs">Pairs</option>
+                                <option value="all">All</option>
+                                <option value="homoz">Homozygous</option>
+                                <option value="mnallele">MNAllele</option>
+                                <option value="robdom">RobDom</option>
+                                <option value="ps:mm/mf/ff">PS:MM/MF/FF</option>
+                            </param>
+
+                            <param name="extra_weighting" type="select" label="Weighting function" >
+                                <option value="equal">Equal</option>
+                                <option value="power:0.5">Power</option>
+                            </param>
+                        </when>
+
+                        <when value="classical" >
+                            <conditional name="cond_customfreqs" >
+                                <param name="opt_custom_freqs" type="select" label="Use custom frequencies instead of datafile" >
+                                    <option value="yes" >Yes</option>
+                                    <option value="no" selected="true" >No</option>
+                                </param>
+                                <when value="no" />
+                                <when value="yes" >
+                                    <param name="extra_linkage_par_freq" type="float" value="0" min="0" max="1" label="Frequency" />
+                                    <param name="extra_linkage_par_pen" type="text" value="p0/p1/p2" label="Penetrance" />
+                                </when>
+                            </conditional>
+                            <param name="extra_linkage_par_het" type="float" value="" label="HET Frequency (leave blank for dynamic)" />
+                        </when>
+                    </conditional>
+
+                    <conditional name="cond_steps" >
+                        <param name="extra_steps_type" type="select" label="Step Type" >
+                            <option value="STEPS">Calculations between adjacent markers</option>
+                            <option value="STEPFILE">Calculations at positions set in file</option>
+                            <option value="MAXSTEPLENGTH">Calculations at periodic (cM) intervals</option>
+                        </param>
+                        <when value="STEPS">
+                            <param name="extra_steps" type="integer" min="1" value="2" label="# Steps" />
+                        </when>
+                        <when value="STEPFILE">
+                            <param name="inp_stepfile" type="data" format="txt" label="Step file" />
+                        </when>
+                        <when value="MAXSTEPLENGTH">
+                            <param name="extra_maxstep" type="float" min="1" value="2" label="cM" />
+                        </when>
+                    </conditional>
+                </section>
+            </when>
+        </conditional>
+
+        <param name="opt_xlinked" type="select" label="Disease model" >
+            <option value="">Autosomal</option>
+            <option value="X">X-Linked</option>
+        </param>
+
+        <param name="opt_entropy" type="boolean" truevalue="on" falsevalue="off" checked="false" label="Entropy" />
+        <param name="opt_nplexactp" type="boolean" truevalue="on" falsevalue="off" checked="false" label="Use exact P-values" />
+
+        <conditional name="cond_pairwise" >
+            <param name="opt_pairwise" type="select" label="Perform Pairwise Analysis?" >
+                <option value="yes" >Yes</option>
+                <option value="no" selected="true" >No</option>
+            </param>
+
+            <when value="no"/>
+            <when value="yes" >
+                <param name="extra_pairwise_type" type="select" label="Weighting" >
+                    <option value="all">All</option>
+                    <option value="genotype">Genotype</option>
+                    <option value="affected">Affected</option>
+                    <option value="informative">Informative</option>
+                </param>
+            </when>
+        </conditional>
+
+        <conditional name="cond_sim" >
+            <param name="opt_sim" type="select" label="Simulate multipoint data?" >
+                <option value="yes" >Yes</option>
+                <option value="no" selected="true" >No</option>
+            </param>
+            <when value="no" />
+            <when value="yes" >
+                <param name="extra_sim_dloc" type="float" value="" min="0" label="Disease Locus (cM). Leave blank for unlinked disease locus." />
+                <param name="extra_sim_npre" type="integer" value="1" label="Number of prefiles to generate" />
+                <param name="extra_sim_rep" type="integer" value="1" label="How many times to repeat family pattern" />
+                <param name="extra_sim_err" type="float" value="0" min="0" label="Error Rate" />
+                <param name="extra_sim_yield" type="float" value="1" label="Genotype Yield" />
+                <param name="extra_sim_het" type="float" value="0" label="HET probability" />
+            </when>
+        </conditional>
+        <param name="opt_sexspecific" type="boolean" truevalue="on" falsevalue="off" value="false" label="Use Sex-Specific Penetrances (specified in data file)" help="Note that you will need to include sex-specific penetrances in your data input file for this to work." />
+        <param name="opt_unit" type="boolean" truevalue="centimorgan" falsevalue="recombination" value="false" label="Datafile uses centimorgan distances instead of recombination frequencies" />
+    </inputs>
+
+    <outputs>
+        <data name="out_ihaplo" format="allegro_haplo" label="${tool.name} on ${on_string}: Haplotypes" />
+        <data name="out_fparam" format="allegro_linkage" label="${tool.name} on ${on_string}: Linkage" />
+        <data name="out_founder" format="allegro_descent" label="${tool.name} on ${on_string}: Descent" />
+        <data name="out_linexp" format="txt" label="${tool.name} on ${on_string}: Linear Expression" />
+        <data name="out_combined_cross" format="txt" label="${tool.name} on ${on_string}: Combined Crossovers" />
+    </outputs>
+
+    <tests>
+        <test><!-- Default Haplotypes -->
+            <expand macro="macro_inputs" />
+            
+            <param name="extra_linkage_type" value="classical" />
+            <param name="extra_linkage_mptspt" value="mpt" />
+            <param name="opt_haplotypes" value="yes" />
+
+            <output name="out_ihaplo" >
+                <assert_contents>
+                    <has_text_matching expression="1\s+206003\s+111\s+112(\s+[012])+" />
+                </assert_contents>
+            </output>
+        </test>
+        <test><!-- Linkage with custom steps-->
+            <expand macro="macro_inputs" />
+            
+            <param name="extra_linkage_type" value="classical" />
+            <param name="extra_linkage_mptspt" value="mpt" />
+            <param name="extra_linkage_mptspt" value="mpt" />
+            <param name="extra_steps" value="3" />
+            <param name="extra_maxstep" value="30" />
+
+
+            <output name="out_fparam" >
+                <assert_contents>
+                    <has_text_matching expression="1(\s+[-0-9.]+){2}\s+rs2822572" />
+                </assert_contents>
+            </output>
+        </test>
+        <test><!-- Single-point linear expression test with power weights -->
+            <expand macro="macro_inputs" />
+            
+            <param name="extra_linkage_type" value="allele_sharing" />
+            <param name="extra_linkage_mptspt" value="spt" />
+            <param name="extra_linkage_linexp" value="lin" />
+            <param name="extra_linkage_scoring" value="homoz" />
+            <param name="extra_weighting" value="power:50" />
+                       
+            <output name="out_fparam" >
+                <assert_contents>
+                    <has_text_matching expression='(\-\d+\.\d+\s+)+rs2822696' />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+Allegro is a computer program for multipoint genetic linkage analysis and related calculations. Allegro can do both classical parametric linkage analysis and analysis based on allele sharing models. In addition, Allegro estimates total number of recombinations between markers, computes posterior IBD sharing probabilities, re-constructs haplotypes and does two types of simulation. Thus Allegro includes the basic functionality of the well known Genehunter program (Kruglyak et al. 1996). It can analyse pedigrees of moderate size,and it can handle many markers. The biggest advantages of Allegro over Genehunterar the allele sharing models that it provides and a much shorter execution time.
+    </help>
+    <citations>
+        <citation type="doi">10.1038/ng1005-1015</citation>
+        <citation type="doi">10.1038/75514</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 8c29e3621475 test-data/datain.21
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/datain.21	Sat Dec 09 06:39:42 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
+ 0.1  0.000699  0.000751  0.001625  0.000626  0.000902  0.001785  0.000970  0.001647  0.001241  0.000538  0.001138  0.000606  0.000504  0.000859  0.000504  0.001582  0.000504  0.001393  0.000552  0.001420  0.000533  0.000638  0.000596  0.000705  0.000567  0.001541  0.003324  0.001431  0.000703  0.001346  0.001978  0.000846  0.000598  0.000547  0.000887  0.002148  0.000873  0.001850  0.000800  0.000771  0.000785  0.000544  0.001836  0.000556  0.001838  0.000854  0.001010  0.001044  0.000913  0.002090  0.000800  0.003138  0.001451  0.000676  0.001048  0.005681  0.001075  0.001309  0.002052  0.002013  0.001811  0.001415  0.000890  0.000620  0.001575  0.000961  0.000590  0.000592  0.001485  0.000536  0.000692  0.003783  0.000504  0.001024  0.001595  0.002290  0.002725  0.001189  0.000622  0.000829  0.000530  0.001256  0.002036  0.001575  0.001122  0.000963  0.000909  0.001877  0.001159  0.000839  0.002653  0.000589  0.001128  0.001040  0.000572  0.000756  0.000518  0.000842  0.000642  0.000931  0.000852  0.000540  0.001125  0.002038  0.000547  0.000527  0.002150  0.001016  0.000564  0.000620  0.000526  0.001174  0.001572  0.000655  0.000776  0.000504  0.000521  0.000512  0.000629  0.000570  0.000515  0.001805  0.001103  0.001429  0.001403  0.003479  0.001278  0.001141  0.000866  0.000947  0.000979  0.000564  0.003575  0.001911  0.001271  0.000622  0.001919  0.000572  0.000855  0.001534  0.000840  0.000885  0.000505  0.000773  0.002112  0.000568  0.000553  0.000694  0.001058  0.000627  0.002328  0.002346  0.001778  0.000921  0.000535  0.000610  0.000785  0.000673  0.000625  0.000566  0.002054  0.001007  0.000625  0.000545  0.000733  0.000851  0.000544  0.001300  0.000559  0.000871  0.000571  0.000574  0.000588  0.000690  0.002225  0.000511  0.000839  0.001752  0.000544  0.001807  0.000633  0.000547  0.001712  0.001575  0.000512  0.000567  0.000586  0.001449  0.000862  0.001286  0.000506  0.000518  0.000545  0.001830  0.000665  0.000949  0.001156  0.001236  0.000501  0.000613  0.000572  0.000545  0.000695  0.000524  0.000578  0.000534  0.000970  0.000525  0.000634  0.000567  0.000523  0.000509  0.002036  0.001219  0.001222  0.002258  0.001873  0.001112  0.000799  0.002594  0.000695  0.000502  0.002240  0.000776  0.000534  0.000528  0.002549  0.000504  0.000538  0.001636  0.000791  0.000812  0.001350  0.000502  0.004374  0.000534  0.000518  0.000588  0.000535  0.000754  0.000555  0.001752  0.004448  0.000885  0.001773  0.000566  0.001217  0.000518  0.000732  0.000922  0.000684  0.000503  0.000685  0.000567  0.000543  0.000506  0.000527  0.001806  0.001391  0.000630  0.000505  0.001327  0.000513  0.000664  0.000529  0.000621  0.001258  0.001421  0.000511  0.002351  0.000501  0.000971  0.001581  0.001360  0.000778  0.000590  0.000685  0.001437  0.001497  0.000590  0.000905  0.000541  0.000503  0.001822  0.000779  0.000877  0.000562  0.000526  0.000625  0.000576  0.000600  0.000633  0.001288  0.001829  0.000504  0.000512  0.001125  0.000553  0.000785  0.000776  0.001828  0.000502  0.001045  0.001246  0.000698  0.000868  0.000518  0.000547  0.000676  0.000598  0.000596  0.000690  0.001273  0.000516  0.000503  0.000997  0.001706  0.000721  0.000533  0.000588  0.001516  0.000518  0.001056  0.000507  0.000502  0.002850  0.000626  0.000507  0.000568  0.001302  0.000633  0.002292  0.000500  0.002014  0.000533  0.001410  0.000595  0.000706  0.001283  0.000699  0.001022  0.000681  0.001685  0.001932  0.000864  0.001435  0.001734  0.000653  0.000832  0.000743  0.001876  0.000751  0.000520  0.001096  0.000558  0.000740  0.001345  0.000549  0.001962  0.000521  0.001245  0.000516  0.000517  0.002282  0.000511  0.000811  0.000722  0.001754  0.000511  0.000550  0.001908  0.000534  0.001669  0.001935  0.001493  0.000521  0.000733  0.000816  0.001478  0.000626  0.000520  0.000578  0.001743  0.000501  0.001703  0.000526  0.000628  0.000540  0.001511  0.001159  0.000523  0.000984  0.002506  0.000619  0.002135  0.001293  0.000559  0.000509  0.000530  0.000621  0.001215  0.000594  0.000945  0.002575  0.000588  0.000588  0.001190  0.000544  0.001123  0.001036  0.000564  0.000514  0.000816  0.000939  0.001210  0.000698  0.000526  0.001199  0.001589  0.002322  0.000500  0.000600  0.000804  0.001471  0.000520  0.000679  0.000669  0.000976  0.000614  0.000676  0.001038  0.000881  0.000790  0.001515  0.002322  0.000535  0.001803  0.002088  0.000883  0.000826  0.000703  0.000743  0.000651  0.001431  0.000923  0.000535  0.001250  0.000957  0.000697  0.001615  0.000817  0.001998  0.000638  0.000531  0.000910  0.001797  0.000571  0.001722  0.003449  0.001449  0.000801  0.001141  0.000504  0.001250  0.001787  0.000573  0.000845  0.000968  0.005449  0.000563  0.000721  0.001198  0.000552  0.001350  0.001014  0.000675  0.000537  0.000533  0.001793  0.000817  0.000520  0.002322  0.000551  0.000773  0.001852  0.000526  0.001451  0.000606  0.001702  0.000714  0.000602  0.000608  0.001443  0.000767  0.001225  0.000925  0.000505  0.000753  0.001616  0.001311  0.002005  0.001083  0.000615  0.000579  0.000516  0.001166  0.000934  0.001147  0.001770  0.000501  0.000674  0.001566  0.000736  0.000546  0.001212  0.000502  0.001283  0.000777  0.000782  0.000579  0.000977  0.001867  0.000720  0.002157  0.001494  0.002188  0.001952  0.001566  0.000694  0.001341  0.001138  0.000879  0.000570  0.001607  0.000732  0.000613  0.000502  0.000776  0.000990  0.000737  0.000643  0.000579  0.000625  0.000514  0.000962  0.000690  0.002351  0.001055  0.001971  0.000545  0.000640  0.002772  0.000510  0.000516  0.000636  0.000763  0.001327  0.000871  0.001994  0.000702  0.000581  0.000505  0.000585  0.001833  0.001476  0.000813  0.001382  0.001200  0.000533  0.001116  0.001082  0.001198  0.000976  0.000507  0.000527  0.001056  0.003941  0.001371  0.000501  0.000501
+ 1      2.0  1.0
diff -r 000000000000 -r 8c29e3621475 test-data/map.21
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/map.21	Sat Dec 09 06:39:42 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
+ 21   11.27225313   rs2824669   18457462    86
+ 21   11.36867493   rs2824688   18474751    87
+ 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
+ 21   12.28574212  rs17781453   18653275    94
+ 21   12.38984244    rs978421   18764344    95
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