| Next changeset 1:7fe16841fe35 (2016-03-18) |
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added:
qtlmap_15/._.DS_Store qtlmap_15/._readme.txt qtlmap_15/qtlmap7_15nodes.py qtlmap_15/qtlmap7_15nodes.xml qtlmap_15/readme.txt qtlmap_15/test-data/._.DS_Store qtlmap_15/test-data/input/._.DS_Store qtlmap_15/test-data/input/._parameters.txt qtlmap_15/test-data/input/._qtlcart1.inp qtlmap_15/test-data/input/._qtlcart10.inp qtlmap_15/test-data/input/._qtlcart11.inp qtlmap_15/test-data/input/._qtlcart12.inp qtlmap_15/test-data/input/._qtlcart13.inp qtlmap_15/test-data/input/._qtlcart14.inp qtlmap_15/test-data/input/._qtlcart15.inp qtlmap_15/test-data/input/._qtlcart2.inp qtlmap_15/test-data/input/._qtlcart3.inp qtlmap_15/test-data/input/._qtlcart4.inp qtlmap_15/test-data/input/._qtlcart5.inp qtlmap_15/test-data/input/._qtlcart6.inp qtlmap_15/test-data/input/._qtlcart7.inp qtlmap_15/test-data/input/._qtlcart8.inp qtlmap_15/test-data/input/._qtlcart9.inp qtlmap_15/test-data/input/._qtlcart_original.map.txt qtlmap_15/test-data/input/parameters.txt qtlmap_15/test-data/input/qtlcart1.inp qtlmap_15/test-data/input/qtlcart10.inp qtlmap_15/test-data/input/qtlcart11.inp qtlmap_15/test-data/input/qtlcart12.inp qtlmap_15/test-data/input/qtlcart13.inp qtlmap_15/test-data/input/qtlcart14.inp qtlmap_15/test-data/input/qtlcart15.inp qtlmap_15/test-data/input/qtlcart2.inp qtlmap_15/test-data/input/qtlcart3.inp qtlmap_15/test-data/input/qtlcart4.inp qtlmap_15/test-data/input/qtlcart5.inp qtlmap_15/test-data/input/qtlcart6.inp qtlmap_15/test-data/input/qtlcart7.inp qtlmap_15/test-data/input/qtlcart8.inp qtlmap_15/test-data/input/qtlcart9.inp qtlmap_15/test-data/input/qtlcart_original.map.txt qtlmap_15/test-data/output/._qtl_out_1.txt qtlmap_15/test-data/output/._qtl_out_10.txt qtlmap_15/test-data/output/._qtl_out_11.txt qtlmap_15/test-data/output/._qtl_out_12.txt qtlmap_15/test-data/output/._qtl_out_13.txt qtlmap_15/test-data/output/._qtl_out_14.txt qtlmap_15/test-data/output/._qtl_out_15.txt qtlmap_15/test-data/output/._qtl_out_2.txt qtlmap_15/test-data/output/._qtl_out_3.txt qtlmap_15/test-data/output/._qtl_out_4.txt qtlmap_15/test-data/output/._qtl_out_5.txt qtlmap_15/test-data/output/._qtl_out_6.txt qtlmap_15/test-data/output/._qtl_out_7.txt qtlmap_15/test-data/output/._qtl_out_8.txt qtlmap_15/test-data/output/._qtl_out_9.txt qtlmap_15/test-data/output/qtl_out_1.txt qtlmap_15/test-data/output/qtl_out_10.txt qtlmap_15/test-data/output/qtl_out_11.txt qtlmap_15/test-data/output/qtl_out_12.txt qtlmap_15/test-data/output/qtl_out_13.txt qtlmap_15/test-data/output/qtl_out_14.txt qtlmap_15/test-data/output/qtl_out_15.txt qtlmap_15/test-data/output/qtl_out_2.txt qtlmap_15/test-data/output/qtl_out_3.txt qtlmap_15/test-data/output/qtl_out_4.txt qtlmap_15/test-data/output/qtl_out_5.txt qtlmap_15/test-data/output/qtl_out_6.txt qtlmap_15/test-data/output/qtl_out_7.txt qtlmap_15/test-data/output/qtl_out_8.txt qtlmap_15/test-data/output/qtl_out_9.txt |
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| diff -r 000000000000 -r fa0693cf076b qtlmap_15/qtlmap7_15nodes.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/qtlmap7_15nodes.py Fri Mar 18 05:51:39 2016 -0400 |
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| b'@@ -0,0 +1,469 @@\n+"""\n+@summary: MAP and PARSE\n+@version 7\n+\n+"""\n+# MAPPER --> save only QTL output\n+\n+# Input: qtlcart.inp\n+# qtlcart.map\n+# \t parameters.txt\n+\n+# Output: QTLs_total.txt\n+\n+import optparse, sys\n+import tempfile\n+import re\n+\n+def stop_err( msg ):\n+\tsys.stderr.write( "%s\\n" % msg )\n+\tsys.exit()\n+ \n+def __main__():\n+\tparser = optparse.OptionParser()\n+\tparser.add_option("-i", "--input1", default=None, dest="input1", \n+\t\t\t help="qtlcart.inp file")\n+\tparser.add_option("-j", "--input2", default=None, dest="input2", \n+\t\t\t help="qtlcart.map file")\n+\tparser.add_option("-k", "--input3", default=None, dest="input3", \n+\t\t\t help="parameters.txt file")\n+ \n+\tparser.add_option("-o", "--output1", default=None, dest="output1", \n+\t\t\t help="QTLs_total.txt file")\n+\t(options, args) = parser.parse_args()\n+\t\n+\ttry:\n+\t open(options.input1, "r").close()\n+\texcept TypeError, e:\n+\t stop_err("You need to supply the qtlcart.inp file:\\n" + str(e))\n+\texcept IOError, e:\n+\t stop_err("Can not open the qtlcart.inp file:\\n" + str(e))\n+ \n+\ttry:\n+\t open(options.input2, "r").close()\n+\texcept TypeError, e:\n+\t stop_err("You need to supply the qtlcart.map file:\\n" + str(e))\n+\texcept IOError, e:\n+\t stop_err("Can not open the qtlcart.map file:\\n" + str(e))\n+\n+\ttry:\n+\t open(options.input3, "r").close()\n+\texcept TypeError, e:\n+\t stop_err("You need to supply the parameters.txt file:\\n" + str(e))\n+\texcept IOError, e:\n+\t stop_err("Can not open the parameters.txt file:\\n" + str(e))\n+\t\n+\t######################################################################\n+\t# submit.py\n+\t######################################################################\n+\t\n+\timport subprocess\n+\timport os\n+\t\n+\t# Create temp direcotry\n+\ttempdir = tempfile.mkdtemp()\n+\t#print tempdir\n+\t\n+\ts = "cp %s %s/parameters.txt" %(options.input3, tempdir)\n+\tsubprocess.call(s, shell=True)\n+\tparamters_file = open(tempdir+"/parameters.txt", "r")\n+\tparvalues = []\n+\tfor line in paramters_file:\n+\t\tl = line.strip().split("\\t")\n+\t\tif l[0] == "SRmodel":\n+\t\t\tSRmodel = l[1]\n+\t\tif l[0] == "Zmodel":\n+\t\t\tZmodel = l[1]\n+\t\tif l[0] == "threshold":\n+\t\t\tthreshold = l[1]\n+\t\tif l[0] == "walking_speed":\n+\t\t\twalking_speed = l[1]\n+\t\tif l[0] == "window_size":\n+\t\t\twindow_size = l[1]\n+\t\tif l[0] == "minimum_cM_between_QTL":\n+\t\t\tminimum_cM_between_QTL = l[1]\n+\tparamters_file.close()\t\t\n+\n+\t# copy INPUT file to the temp directory\n+\ts = "cp %s %s/qtlcart.inp" %(options.input1, tempdir)\n+\tsubprocess.call(s, shell=True)\n+\ts = "cp %s %s/qtlcart.map" %(options.input2, tempdir)\n+\tsubprocess.call(s, shell=True)\n+\t\n+ f=open(tempdir+"/qtlcart.inp", "r")\n+\tln=f.readlines()\n+ f.close()\n+ \n+ if ln[0] == "NA":\n+\t\tf1=open(tempdir+"/QTLs_total_parsed_LOD.txt", "w")\n+\t\tf1.write("")\n+\t\tf1.close()\n+\t\tos.system("mv %s/QTLs_total_parsed_LOD.txt %s" %(tempdir,options.output1))\n+\t\t#os.system("mv %s/qtlcart.rc %s" %(tempdir,options.output2))\n+ else:\n+\t\tinstruction = "/cluster1/bin/Rcross -i %s/qtlcart.inp -o %s/qtlcart.cro -A -V" %(tempdir, tempdir)\n+\t\tos.system(instruction)\n+\t\t\n+\t\tinstruction = "/cluster1/bin/SRmapqtl -i %s/qtlcart.cro -e %s/SRqtlcart.log -o %s/qtlcart.sr -m %s/qtlcart.map -M %s -t 9999999999 -A -V" %(tempdir, tempdir, tempdir, tempdir, str(SRmodel))\n+\t\tos.system(instruction) \n+\t\t\n+\t\tinstruction = "/cluster1/bin/Zmapqtl -i %s/qtlcart.cro -o %s/qtlcart.z -m %s/qtlcart.map -S %s/qtlcart.sr -M %s -d %s -w %s -t 9999999999 -A -V" %(tempdir, tempdir, tempdir, tempdir, str(Zmodel), str(walking_speed), str(window_size))\n+\t\tos.system(instruction)\n+\t\t\n+\t\t#instruction = "/cluster1/bin/Eqtl -m %s/qtlcart.map -z %s/qtlcart.z -e %s/Eqtlcart.log -o %s/qtlcart.eqt -S %s -A -V" %(tempdir, tempdir, tempdir, tempdir, str(threshold))\n+\t\t#os.system(instruction)\n+\n+\t\t#####################\n+\t\t# parse_eqt_file.py\n+\t\t#####################\n+\t\t\n+\t\tinfile = open(tempdir+"/qtlcart.z","r")\n+\t\toutfile = open(tempdir+"/QTLs_total_parsed.txt","w")\n+\t\t\n+\t\toutfile.write("trait_'..b'2 = float(z_dict[left_id][3]) # small lod\n+\t\t\tl1 = float(z_dict[left_id+1][2]) # large position\n+\t\t\tl2 = float(z_dict[left_id+1][3]) # large lod\n+\t\t\t\n+\t\t\tif (l2-s2) != 0:\n+\t\t\t\tlod2_L_pos = round(((lod2-s2)*(l1-s1)/(l2-s2))+s1,4)\n+\t\t\telse:\n+\t\t\t\tlod2_L_pos = round(((lod2-s2)*(l1-s1)/(0.00001))+s1,4)\n+\t\t\t\n+\t\t\tlod2_L_m = z_dict[left_id][1]\n+\t\t\tif lod2_L_pos < 0:\n+\t\t\t lod2_L_pos = z_dict[1][2]\n+\t\t\t lod2_L_m = z_dict[2][1]\n+\t\t\tif ((lod2_L_pos >= s1) and (lod2_L_pos <= l1)):\n+\t\t\t pass\n+\t\t\telse:\n+\t\t\t lod2_L_pos = z_dict[1][2]\n+\t\t\t lod2_L_m = z_dict[1][1] \n+\t\t else:\n+\t\t\tlod2_L_pos = z_dict[1][2]\n+\t\t\tlod2_L_m = z_dict[1][1]\n+\t\t ans.append(lod2_L_m)\n+\t\t ans.append(lod2_L_pos)\n+\t\t \n+\t\t \n+\t\t # lod2_R calculation\n+\t\t #print "==== lod2_R"\n+\t\t add = 1\n+\t\t right_id = peak_id+1\n+\t\t if right_id <= max(z_dict.keys()):\n+\t\t\twhile (z_dict[peak_id+add][3] > lod2) and (right_id < max(z_dict.keys())):\n+\t\t\t add += 1\n+\t\t\t right_id = peak_id+add\n+\t\t\t\n+\t\t\ts1 = float(z_dict[right_id-1][2]) # small position\n+\t\t\ts2 = float(z_dict[right_id-1][3]) # small lod\n+\t\t\tl1 = float(z_dict[right_id][2]) # large position\n+\t\t\tl2 = float(z_dict[right_id][3]) # large lod\n+\t\t\t\n+\t\t\tif (l2-s2) != 0:\n+\t\t\t\tlod2_R_pos = round(((lod2-s2)*(l1-s1)/(l2-s2))+s1,4)\n+\t\t\telse:\n+\t\t\t\tlod2_R_pos = round(((lod2-s2)*(l1-s1)/(0.00001))+s1,4)\n+\t\t\tlod2_R_m = z_dict[right_id-1][1]\n+\n+\t\t\tif lod2_R_pos > float(z_dict[max(z_dict.keys())][2]):\n+\t\t\t lod2_R_pos = z_dict[max(z_dict.keys())][2]\n+\t\t\t lod2_R_m = z_dict[max(z_dict.keys())][1]\n+\t\t\tif ((lod2_R_pos >= s1) and (lod2_R_pos <= l1)):\n+\t\t\t pass\n+\t\t\telse:\n+\t\t\t lod2_R_pos = z_dict[max(z_dict.keys())][2]\n+\t\t\t lod2_R_m = z_dict[max(z_dict.keys())][1]\n+\t\t else:\n+\t\t\tlod2_R_pos = z_dict[max(z_dict.keys())][2]\n+\t\t\tlod2_R_m = z_dict[max(z_dict.keys())][1]\n+\t\t ans.append(lod2_R_m)\n+\t\t ans.append(lod2_R_pos)\n+\t\t \n+\t\t eQTL_dict[i].append(ans)\n+\t\t \n+\t\thead = ["LOD1_L_m","LOD1_L_pos","LOD1_R_m","LOD1_R_pos","LOD2_L_m","LOD2_L_pos","LOD2_R_m","LOD2_R_pos"]\n+\t\t\n+\t\ti = -1\n+\t\teqtfile = open(tempdir+"/QTLs_total_parsed.txt","r")\n+\t\tfor line in eqtfile:\n+\t\t i += 1\n+\t\t if i == 0:\n+\t\t\toutfile.write(line.strip()+"\\t"+"\\t".join(head)+"\\n")\n+\t\t else: \n+\t\t\toutfile.write(line.strip()+"\\t"+"\\t".join(str(x) for x in eQTL_dict[i][5])+"\\n")\n+\t\t \n+\t\teqtfile.close()\n+\t\toutfile.close()\n+\t\t\n+\t\t#####################\n+\t\t# merge_QTLs.py\n+\t\t#####################\n+\t\t\n+\t\tinfile = open(tempdir+"/QTLs_total_parsed_LOD.txt","r")\n+\t\toutfile = open(tempdir+"/QTLs_total_parsed_LOD_merged.txt","w")\n+\t\t\n+\t\ttest = ""\n+\t\tfor line in infile:\n+\t\t l = line.strip().split("\\t")\n+\t\t if l[0] == "trait_name":\n+\t\t\tkeep = l\n+\t\t else:\n+\t\t\ttest = l\n+\t\t\tif keep[0] != test[0]: # if trait names are not the same ---> write keep\n+\t\t\t\tif keep[0] != "trait_name": # no not include header, only when integrate\n+\t\t\t\t\toutfile.write("\\t".join(keep)+"\\n")\n+\t\t\t\tkeep = test\n+\t\t\telse:\n+\t\t\t if keep[3] != test[3]: # if chrs are not the same --> write keep \n+\t\t\t\toutfile.write("\\t".join(keep)+"\\n")\n+\t\t\t\tkeep = test\n+\t\t\t else:\n+\t\t\t\tif not (((float(keep[11])<0) and (float(test[11])<0)) or ((float(keep[11])>0) and (float(test[11])>0))): # if additive signs are not the same --> write keep \n+\t\t\t\t outfile.write("\\t".join(keep)+"\\n")\n+\t\t\t\t keep = test\n+\t\t\t\telse:\n+\t\t\t\t #print str((abs(float(test[5])*100-float(keep[5])*100)))\n+\t\t\t\t if not (abs(float(test[5])*100-float(keep[5])*100)<float(minimum_cM_between_QTL)): #if minimum cM between QTLs > 20 --> write keep\n+\t\t\t\t\toutfile.write("\\t".join(keep)+"\\n")\n+\t\t\t\t\tkeep = test\n+\t\t\t\t else:\n+\t\t\t\t\tif (float(keep[7])<float(test[7])): #if LOD(keep) > LOD(test) --> new keep\n+\t\t\t\t\t keep = test\n+\t\t\n+\t\tif l[0] != "trait_name":\n+\t\t\toutfile.write("\\t".join(keep)+"\\n")\n+\t\t\t\t\t\n+\t\tinfile.close()\n+\t\toutfile.close()\n+\t\t\t\t\n+\t\t\t\t\t\t\n+\t\tos.system("mv %s/QTLs_total_parsed_LOD_merged.txt %s" %(tempdir,options.output1))\n+\t\n+if __name__=="__main__": \n+ __main__()\n+\n+\n' |
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| diff -r 000000000000 -r fa0693cf076b qtlmap_15/qtlmap7_15nodes.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/qtlmap7_15nodes.xml Fri Mar 18 05:51:39 2016 -0400 |
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| @@ -0,0 +1,40 @@ +<tool id="qtlmap7_15nodes" name="Run QTL Cartographer" version="7.0.0"> + <description> and parse the results</description> + <command interpreter="python"> + qtlmap7_15nodes.py --input1 $input1 --input2 $input2 --input3 $input3 --output1 $output1 + </command> + <inputs> + <param label="Phenotype-genotype (.inp) file" name="input1" type="data" format="txt" help="A .inp file with all genotype and phenotype information"></param> + <param label="QTL Cartographer map file" name="input2" type="data" format="txt" help="A .inp file with all genotype and phenotype information"></param> + <param label="Parameters file" name="input3" type="data" format="txt" help="Parameters file with the values of all the parameters for QTL mapping"></param> + </inputs> + <outputs> + <data format="tabular" name="output1" /> + </outputs> + <requirements> + </requirements> + <tests> + <test> + </test> + </tests> + <help> + +**What it does** + +Runs QTL Cartographer for QTL/eQTL mapping. Parse the results. + +**Example output file** + +eQTL results file, each row correspond to an eQTL (21 columns; only a part of the file is shown):: + + trait_name trait_number eQTL_number chr peak_marker peak_position peak_LR peak_LOD R2 TR2 S additive dominance LOD1_L_m LOD1_L_pos LOD1_R_m LOD1_R_pos LOD2_L_m LOD2_L_pos LOD2_R_m LOD2_R_pos + geneA 4 2 3 15 79.31 14.576 3.162992 0.1093 0.1915 5.2649 -0.0602 0 12 0.6318 15 0.8678 11 0.5984 15 0.8941 + geneB 5 1 6 7 54.41 12.0029 2.6046293 0.0833 0.1621 5.0323 0.0516 0 6 0.4803 7 0.6296 5 0.4237 7 0.6509 + geneC 6 1 1 12 81.5 13.2053 2.8655501 0.082 0.2517 154.622 -0.0513 0 11 0.7835 12 0.815 10 0.6549 12 0.815 + geneC 6 2 5 6 33.92 12.4418 2.6998706 0.0881 0.2653 161.127 0.0546 0 4 0.2652 6 0.4058 2 0.1031 7 0.4629 + geneF 11 1 9 4 11.74 14.4418 3.1338706 0.0937 0.252 72.2489 -0.0562 0 1 0.0014 4 0.1995 1 0.0001 4 0.2035 + geneH 12 2 1 9 43.66 16.9545 3.6791265 0.092 0.3558 0.1466 0.0544 0 8 0.4159 9 0.5408 5 0.3295 9 0.5987 + geneJ 13 1 7 11 66.41 15.6251 3.3906467 0.0965 0.2625 8.2335 -0.0558 0 9 0.5515 11 0.7408 9 0.5464 12 0.7631 + + </help> +</tool> |
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| diff -r 000000000000 -r fa0693cf076b qtlmap_15/readme.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/readme.txt Fri Mar 18 05:51:39 2016 -0400 |
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| @@ -0,0 +1,23 @@ +====================================================================== +qtlmap_15 +====================================================================== +### This is the second tool in the eQTL mapper pipeline: +split_15, qtlmap_15, save_z_15, integrate_15 + +Link to the workflow (for import): http://chewbacca.bi.up.ac.za:8080/u/nanette/w/15-parallel + +QTL Cartographer is employed for eQTL mapping. The results are parsed. + +This tool must be executed 15 times in parallel; every time with a different .inp input file (every time the .map and parameters.txt input files are used). Each execution will produce one .txt output file. + +--------------- +Installation +--------------- + +The eQTL mapper pipeline is available for: +* command line usage +* integration into Galaxy servers + + +Requirements: Python 2.7 + QTL Cartographer 1.17 \ No newline at end of file |
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| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/input/._qtlcart8.inp |
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| Binary file qtlmap_15/test-data/input/._qtlcart8.inp has changed |
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| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/input/._qtlcart9.inp |
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| Binary file qtlmap_15/test-data/input/._qtlcart9.inp has changed |
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| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/input/._qtlcart_original.map.txt |
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| Binary file qtlmap_15/test-data/input/._qtlcart_original.map.txt has changed |
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| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/input/parameters.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/input/parameters.txt Fri Mar 18 05:51:39 2016 -0400 |
| b |
| @@ -0,0 +1,6 @@ +SRmodel 2 +Zmodel 6 +threshold 11.5 +walking_speed 2.0 +window_size 10.0 +minimum_cM_between_QTL 20.0 |
| b |
| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/input/qtlcart1.inp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/input/qtlcart1.inp Fri Mar 18 05:51:39 2016 -0400 |
| b |
| b'@@ -0,0 +1,692 @@\n+#bycross\n+-SampleSize 100\n+-Cross Ri1\n+-traits 4\n+-otraits 0\n+-missingtrait .\n+-case yes\n+-TranslationTable\n+AA\t2\tA\n+Aa\t1\t*1\n+aa\t0\tB\n+A-\t12\t*2\n+a-\t10\t*3\n+--\t-1\t-\n+-start markers\n+phi056 A A B B A B B A A A B A B A A A A A A A A A B A \n+B B A B - B B A B B - - A B A B A - - A B A A A A B A A A - B A B B - \n+A - B B B B A B A B A B - - A B A B A - B A A A A B A A B A B A A B A \n+B A B A A B \n+bnl5.62 A A - B A B B A B A B A B B A A A A A A A A B A \n+B A - B - A A A B A - A A B A B A B A A B A A A - B A A A B B A B B - \n+A A B B B B A B A B A A A - A B A B B A B A A - A B A A B A B B A B A \n+B A B A A B \n+umc1041 A A B B A A B A B B A B B A - A B A A A A B B A \n+A A B B - A A A B A B B B B B A - B A A B A A A - A A B - - B A B B B \n+A A B A B A A B A B A A A B A B A B A A B A - A A B A A B A B A A A A \n+B A B B A B \n+umc157a A A B A B A B A A B B - B A A A B - B A A A A A \n+A B B B - A A A B A A A B B A A B B B A A - B A A B A B A A B A A B B \n+A A B A B A A B B A A A A B A B B A B A A A A B A A B A B A B B A B A \n+B A B B B B \n+bnlg1178 A A A A B A B A A B B - B B A A B B B A A B A A \n+A B B B B A A A B A A A B B A A B B B A A - B A B - A B - A A - A B - \n+A A B A A A A B A A A A B B A - A A B B A A A B A A B - B - B B A B A \n+B A B B B B \n+bnlg1429 A A A A B A B A A B B B B B A A B - B A A B A A \n+A B B B B A A A B A A A B B A A B A B A A - B A B B A B - - A A B B - \n+B A B A A A A B A A A A A B A - A A B A A A A B A A B A B A A B A B A \n+B A B B B B \n+bnlg1627 A A A A B B A A B B A B B A A A B B B A A B A A \n+A B - B B A A A B A A A B B A A B A B A A - B A B B A B B - - A B B - \n+A A B A A A A B A B A A A B A B A A B A A A A B A A B A A A A B A B A \n+A A B B B B \n+umc11a A A - A B B B A B B A A B A A B B B B A A A - B \n+A B B B A B A A B B B A B B B A B A B A A B B A B - B B A B A B A B B \n+A A B B A A A B - B A A A B A B B A B A B - A B A A B B A B B - A B A \n+B A B B B B \n+bnlg439 A A A A B B A A B B A A - A A B B B B A A A B B \n+A B A B A A A A B B B A B B B B A A B A A B A B B - - B A B A B A B B \n+A B B A A A A B - B B A B B A - B B B B A A A B A - B A B B B - B - A \n+A A B B B B \n+bnlg2238 A A A - B B A A B B A B A A A B B A A A A A A B \n+A B A B A A A A B B B A A B B A A A - A A B A B B A A B A B A B - B B \n+A B B B A A A B B B B A A B A B B B B A A - A A A A A A A A A A B A A \n+A A - B B B \n+Bnlg1811_U A A A B B A A B B B B B A A A A B A A A A A A B \n+A B A B B B A A B B A A A B B A B A A A B B B B A A B B A B A B A B B \n+A B B B A A A B B B B A A B A B B B B A A A A B - B A B B B A A B A A \n+A A B B A B \n+bnlg2086 A B A A A A A A B B B B A A B - B A A B A A A B \n+A B A B B B A A B A B A A B B B B A A B B - A B B A B B A B B B A B B \n+B B B B A A A B B B A A A B B B - B B A - A A B B A A B B B A A B A A \n+A A A B A B \n+csu61b B B - A B A A A B B B B A B A - B B B B - B A B \n+B A A B B A A A B A B A A B B B B A - B A A - B - B B B A B B B A B B \n+A B B A A A A B B B A B A B A B - B B A - - A B A A - B B B A - B - A \n+A A B B A B \n+bnlg1057 B B A A A A B A B B B B A B A - B B A B B B B B \n+A B A B B A A A - A B A A B B B A A - A A A - B A - B B A - B B A B B \n+A B - A A A A - B A A B A B A B A B B A - B A B A A - B B B A - B - A \n+A A B B A B \n+umc1122 A B A A B A B A B B A B B B A A A B A B A B B A \n+B B A B B B A A B A B A A B B B A A B A A A B B A B B A A A B A A B A \n+A B A A A A B A B A B B A B A B A B B A A A B B A B B B B B B B B B B \n+A A B A A B \n+Bnlg615_U A A B A B B A A B A A B A B A B A B A A A B B B \n+B A A A B A A B B B B A A B B B A A B A A B B B A B B A A - B - A B A \n+A A B A B A B B B A B B A B - B A B B A A A B A A B B B A B B B B B B \n+A A B A A B \n+umc1128 A B B A B B B B B B B A A B A B A B A B A B B A \n+A A B A B A A B B B B A A B B B A A B A A B B B '..b' B A A A A A A A A A A A A A - B A A A A \n+B B B A A A \n+umc182 B B A B A B B A A B B B B B A A B A A B B A A B \n+A A B A B A B A B B B B B A B A A B A B A - A A B A B A B A B A A - B \n+A B B A A B A B B A A A A A A B A B A A A B A A A A A B A B B B A A A \n+B B B A B A \n+bnlg236 B A A B A B A A A B B A B B A A A A A B B A A B \n+A A B A B B B A B B B B B A B A A B A B A A A B B A B A B B B A A A B \n+A B B A A A A B B A A A A A A B A B A A A B A B A - A B A B B A A A A \n+A B B A B A \n+bnl7.49a B A - B B A A - A A A - A B A A A A A B B A A B \n+A - B A B B - A A B B B - B B A A A A A A - A B B A B A B B B A A - B \n+B A A A A B A A B A B A A A A B A B A A B - A - A B - B - B B - A A A \n+A B B A B A \n+bnlg1450 A A A B A B A A A B - A A B A B A A A B A A A B \n+A B B - A B B A A B B B B B B A A B A A A - A A B A B A B A B A B - B \n+B B A B A B A A - A B A B A B B A B A B B A A B A A A B A B B A B A A \n+A B A A B A \n+umc1038 A A A B B B A B B B B A B A A B A A A B A B A B \n+A B B B A A A A B A B B B - A A - A - B A B B A B B B A B A B A B - B \n+B B B B A B A B A A B A - A B B B B A B A A B B A A A B - B A B B B A \n+A B A A B - \n+-stop markers\n+-start traits\n+A_92_P039116\t2281.96\t1818.56\t1371.65\t2512.19\t2454.61\t1407.59\t1601.49\t1688.41\t2206.74\t2710.41\t2129.76\t2525.04\t2379.98\t1993.47\t2531.15\t3692.6\t1855.2\t2459.9\t2050.98\t2753.6\t2665.4\t2895.98\t2573.6\t1828.64\t1740.54\t2093.74\t1916.84\t3316.19\t2008.14\t2396.59\t1789.22\t2469.46\t906.54\t2526.57\t2144.33\t2659.07\t1789.72\t2934.56\t2263.96\t1306.36\t1937.21\t1767.7\t1487.56\t1166.91\t5466.83\t4310.64\t1818.28\t2994.05\t1849.14\t2347.48\t2321.16\t2094.86\t1721.59\t1882.73\t2867.4\t2612.62\t2253.14\t1592.96\t2083.23\t2692.6\t2509.63\t2066.2\t2424.42\t1686.29\t362.32\t293.06\t.\t.\t2100.05\t2681.62\t1858.03\t2697.57\t2166.74\t1724.63\t2481.74\t1603.17\t3067.99\t2798.53\t2281.45\t1871.57\t1618.35\t1379.8\t1643.28\t1789.6\t1980.56\t2379.44\t2321.6\t2101.61\t1933.41\t2038.66\t2756.87\t3021.04\t2094.74\t2145.76\t1747.23\t2507.51\t1532.46\t1668.45\t2678.49\t2078.72\n+A_92_P038628\t421.16\t298.69\t.\t.\t279.28\t1327.26\t3411.8\t3224.54\t621.31\t1887.82\t287.36\t3940.29\t588.77\t2902.94\t882.19\t637.98\t2242.22\t1183.81\t998.47\t997.04\t852.56\t1272.68\t4073.05\t2538.43\t1975.92\t5554.46\t.\t.\t1730.01\t6312.13\t1895.92\t814.38\t.\t.\t645.11\t692.87\t485.94\t126.03\t170.31\t5073.95\t888.36\t5632.5\t336.63\t2834.07\t1172.51\t3994.7\t473.55\t1989.15\t1510.88\t1119.3\t1059.12\t1574.78\t1375.97\t1795.12\t1317.67\t2094.03\t224.05\t1287.88\t1596.29\t1164.15\t601.26\t1294.09\t.\t.\t185.45\t406.28\t.\t.\t5631.89\t1364.25\t4809.46\t833.64\t1115.37\t1086.36\t1500.51\t2170.72\t496.47\t2060.46\t610.86\t2295.13\t169.09\t1562.86\t290.23\t392.46\t805.77\t3461.2\t869.16\t2311.38\t684.56\t301.57\t1995.32\t3611.68\t2927.37\t1746.3\t7127.65\t389.05\t2011.95\t1356.47\t173.13\t2358.56\n+A_92_P038470\t.\t.\t306.12\t271.93\t.\t.\t236.98\t143.72\t170.3\t312.76\t229.45\t298.21\t227.65\t344.05\t.\t.\t328.8\t380.16\t220.48\t287.71\t460.6\t249.8\t227.21\t268.76\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t178.3\t200.95\t276.16\t217.85\t257.85\t229.89\t245.1\t271.68\t.\t.\t398.31\t271.7\t280.94\t189.82\t.\t.\t.\t.\t278.69\t264.84\t.\t.\t255.73\t178.79\t226.85\t236.66\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t424.18\t213.14\t221.17\t255.55\t140.43\t320.81\t337.44\t191.48\t121.84\t216.32\t.\t.\t.\t.\t.\t.\t217.32\t318.08\t132.52\t269.73\t.\t.\t289.95\t337.03\t.\t.\t214.3\t218.2\n+A_92_P038150\t1254.65\t3027.86\t3568.67\t2328.25\t2658.09\t5904.38\t508.89\t562.91\t2571.63\t1687.29\t1827.08\t683.54\t667.26\t1353.95\t1055.86\t1055.8\t1033.17\t1931.23\t3021.96\t1281.73\t2985.33\t2001.71\t1462.14\t3161.77\t1434.97\t1061.68\t1534.86\t1072.1\t1960.25\t3187.95\t1199.39\t2364.05\t.\t.\t1213.63\t3932.68\t4928.96\t868.78\t2066.84\t1094.89\t1069.9\t4829.58\t1051.42\t1586.8\t2425.9\t5025.65\t1591.74\t1862.72\t1952.75\t1794.9\t1290.89\t1546.34\t4237.36\t1519.65\t1501.43\t2884.71\t1344.15\t971.17\t2066.89\t1053.45\t2659.44\t341.27\t921.43\t4391.73\t490.26\t204.39\t.\t.\t1760.11\t1148.13\t1088.95\t1601.91\t2523.37\t614.03\t1032.29\t937.61\t2873.81\t2882.65\t972.04\t1106.16\t1709.07\t1124.55\t1061.09\t1005.36\t1218.5\t1621.98\t1149.98\t2845.99\t959.91\t896.54\t2579.32\t971.96\t2406.24\t2631.56\t969.18\t2102.81\t2803.89\t621.2\t2052.85\t607.76\n+-stop traits\n+-quit\n+-end\n' |
| b |
| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/input/qtlcart10.inp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/input/qtlcart10.inp Fri Mar 18 05:51:39 2016 -0400 |
| b |
| b'@@ -0,0 +1,692 @@\n+#bycross\n+-SampleSize 100\n+-Cross Ri1\n+-traits 4\n+-otraits 0\n+-missingtrait .\n+-case yes\n+-TranslationTable\n+AA\t2\tA\n+Aa\t1\t*1\n+aa\t0\tB\n+A-\t12\t*2\n+a-\t10\t*3\n+--\t-1\t-\n+-start markers\n+phi056 A A B B A B B A A A B A B A A A A A A A A A B A \n+B B A B - B B A B B - - A B A B A - - A B A A A A B A A A - B A B B - \n+A - B B B B A B A B A B - - A B A B A - B A A A A B A A B A B A A B A \n+B A B A A B \n+bnl5.62 A A - B A B B A B A B A B B A A A A A A A A B A \n+B A - B - A A A B A - A A B A B A B A A B A A A - B A A A B B A B B - \n+A A B B B B A B A B A A A - A B A B B A B A A - A B A A B A B B A B A \n+B A B A A B \n+umc1041 A A B B A A B A B B A B B A - A B A A A A B B A \n+A A B B - A A A B A B B B B B A - B A A B A A A - A A B - - B A B B B \n+A A B A B A A B A B A A A B A B A B A A B A - A A B A A B A B A A A A \n+B A B B A B \n+umc157a A A B A B A B A A B B - B A A A B - B A A A A A \n+A B B B - A A A B A A A B B A A B B B A A - B A A B A B A A B A A B B \n+A A B A B A A B B A A A A B A B B A B A A A A B A A B A B A B B A B A \n+B A B B B B \n+bnlg1178 A A A A B A B A A B B - B B A A B B B A A B A A \n+A B B B B A A A B A A A B B A A B B B A A - B A B - A B - A A - A B - \n+A A B A A A A B A A A A B B A - A A B B A A A B A A B - B - B B A B A \n+B A B B B B \n+bnlg1429 A A A A B A B A A B B B B B A A B - B A A B A A \n+A B B B B A A A B A A A B B A A B A B A A - B A B B A B - - A A B B - \n+B A B A A A A B A A A A A B A - A A B A A A A B A A B A B A A B A B A \n+B A B B B B \n+bnlg1627 A A A A B B A A B B A B B A A A B B B A A B A A \n+A B - B B A A A B A A A B B A A B A B A A - B A B B A B B - - A B B - \n+A A B A A A A B A B A A A B A B A A B A A A A B A A B A A A A B A B A \n+A A B B B B \n+umc11a A A - A B B B A B B A A B A A B B B B A A A - B \n+A B B B A B A A B B B A B B B A B A B A A B B A B - B B A B A B A B B \n+A A B B A A A B - B A A A B A B B A B A B - A B A A B B A B B - A B A \n+B A B B B B \n+bnlg439 A A A A B B A A B B A A - A A B B B B A A A B B \n+A B A B A A A A B B B A B B B B A A B A A B A B B - - B A B A B A B B \n+A B B A A A A B - B B A B B A - B B B B A A A B A - B A B B B - B - A \n+A A B B B B \n+bnlg2238 A A A - B B A A B B A B A A A B B A A A A A A B \n+A B A B A A A A B B B A A B B A A A - A A B A B B A A B A B A B - B B \n+A B B B A A A B B B B A A B A B B B B A A - A A A A A A A A A A B A A \n+A A - B B B \n+Bnlg1811_U A A A B B A A B B B B B A A A A B A A A A A A B \n+A B A B B B A A B B A A A B B A B A A A B B B B A A B B A B A B A B B \n+A B B B A A A B B B B A A B A B B B B A A A A B - B A B B B A A B A A \n+A A B B A B \n+bnlg2086 A B A A A A A A B B B B A A B - B A A B A A A B \n+A B A B B B A A B A B A A B B B B A A B B - A B B A B B A B B B A B B \n+B B B B A A A B B B A A A B B B - B B A - A A B B A A B B B A A B A A \n+A A A B A B \n+csu61b B B - A B A A A B B B B A B A - B B B B - B A B \n+B A A B B A A A B A B A A B B B B A - B A A - B - B B B A B B B A B B \n+A B B A A A A B B B A B A B A B - B B A - - A B A A - B B B A - B - A \n+A A B B A B \n+bnlg1057 B B A A A A B A B B B B A B A - B B A B B B B B \n+A B A B B A A A - A B A A B B B A A - A A A - B A - B B A - B B A B B \n+A B - A A A A - B A A B A B A B A B B A - B A B A A - B B B A - B - A \n+A A B B A B \n+umc1122 A B A A B A B A B B A B B B A A A B A B A B B A \n+B B A B B B A A B A B A A B B B A A B A A A B B A B B A A A B A A B A \n+A B A A A A B A B A B B A B A B A B B A A A B B A B B B B B B B B B B \n+A A B A A B \n+Bnlg615_U A A B A B B A A B A A B A B A B A B A A A B B B \n+B A A A B A A B B B B A A B B B A A B A A B B B A B B A A - B - A B A \n+A A B A B A B B B A B B A B - B A B B A A A B A A B B B A B B B B B B \n+A A B A A B \n+umc1128 A B B A B B B B B B B A A B A B A B A B A B B A \n+A A B A B A A B B B B A A B B B A A B A A B B B '..b' A A A \n+B B B A A A \n+npi232a A B A B A B B A A B B B A B A A A A A A A A A B \n+B A A A B B B A A B A B B A B B A B A B A A A B A A A A B A A A A A B \n+A B A A A A A A B A B A A A B B A A A A A A A A A A A A A A A A A A A \n+B A B A A A \n+umc44a A B A B A B B A A B B B B B A A A A A A A A A B \n+B A B A B A B A A - B B A A B A A B A B A A A A - A - A B A B A A - B \n+A B A A A A A B B A A A A A A B A A A A A A A A A A A A A - B A A A A \n+B B B A A A \n+umc182 B B A B A B B A A B B B B B A A B A A B B A A B \n+A A B A B A B A B B B B B A B A A B A B A - A A B A B A B A B A A - B \n+A B B A A B A B B A A A A A A B A B A A A B A A A A A B A B B B A A A \n+B B B A B A \n+bnlg236 B A A B A B A A A B B A B B A A A A A B B A A B \n+A A B A B B B A B B B B B A B A A B A B A A A B B A B A B B B A A A B \n+A B B A A A A B B A A A A A A B A B A A A B A B A - A B A B B A A A A \n+A B B A B A \n+bnl7.49a B A - B B A A - A A A - A B A A A A A B B A A B \n+A - B A B B - A A B B B - B B A A A A A A - A B B A B A B B B A A - B \n+B A A A A B A A B A B A A A A B A B A A B - A - A B - B - B B - A A A \n+A B B A B A \n+bnlg1450 A A A B A B A A A B - A A B A B A A A B A A A B \n+A B B - A B B A A B B B B B B A A B A A A - A A B A B A B A B A B - B \n+B B A B A B A A - A B A B A B B A B A B B A A B A A A B A B B A B A A \n+A B A A B A \n+umc1038 A A A B B B A B B B B A B A A B A A A B A B A B \n+A B B B A A A A B A B B B - A A - A - B A B B A B B B A B A B A B - B \n+B B B B A B A B A A B A - A B B B B A B A A B B A A A B - B A B B B A \n+A B A A B - \n+-stop markers\n+-start traits\n+A_92_P027554\t1420.84\t904.3\t539.95\t824.49\t.\t.\t319.21\t541.4\t763.32\t486.79\t1255.22\t493.19\t885.45\t364.8\t412.15\t590.54\t1622.04\t1764.66\t1279.09\t1949.54\t2725.2\t1054.76\t1238.13\t1654.82\t454.82\t710.94\t537.29\t1318.01\t.\t.\t777.14\t785.59\t.\t.\t407.51\t1261.05\t1159.45\t671.55\t1413.02\t476.71\t622.08\t1209.84\t625.66\t658.81\t686.88\t700.96\t1030.1\t1343.16\t470.41\t336.37\t767.88\t492.46\t475.01\t592.14\t977.13\t342.24\t511.54\t327.9\t480.61\t998.61\t583.59\t401.51\t397.39\t444.41\t138.07\t358.16\t.\t.\t1890.71\t1293.83\t2012.69\t1810.63\t725.7\t304.55\t1297.99\t992.72\t1937.37\t1233.32\t1297.83\t530.05\t1681.23\t380.11\t786.56\t439.27\t1973.48\t473.11\t706.27\t420.91\t1064.85\t407.46\t942.65\t468.02\t756.24\t710.87\t493.37\t961.76\t395.76\t740.47\t1606.81\t238.27\n+A_92_P027390\t.\t.\t.\t.\t.\t.\t.\t.\t189.15\t184.37\t.\t.\t.\t.\t.\t.\t260.06\t284.92\t304.3\t317.94\t303.64\t387.03\t397.51\t241.29\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t226.86\t429.27\t220.14\t204.92\t222.19\t313.64\t121.59\t138.02\t.\t.\t317.27\t350.6\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t353.3\t340.9\t344.31\t346.47\t.\t.\t147.49\t172.43\t309.57\t220.17\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t344.27\t239.63\t219.74\t138.29\t.\t.\t.\t.\t.\t.\t.\t.\n+A_92_P027072\t12801.81\t11777.3\t6934.4\t9082.94\t12152.09\t6141.11\t5784.71\t6674.97\t7233.03\t10239.4\t8237.54\t10937.62\t6376.59\t6689.66\t8186.97\t14265.01\t7345.35\t8382.14\t11648.42\t6341.45\t17842.34\t15962.47\t10020.16\t6300.57\t9908.49\t6381.59\t6935.54\t16042.29\t7774.3\t11871.72\t13025.69\t7376.31\t5043.88\t11335.57\t13927.36\t12312.93\t6340.98\t12934.33\t7587.56\t13031.13\t12449.21\t6646.99\t5908.11\t7289.7\t5602.13\t7232.1\t8973.91\t13880.56\t5841.57\t8808.6\t8661.5\t6956.57\t13010.87\t5773\t8409.56\t6956.12\t9725.49\t4469.11\t11071.72\t11827.56\t7179.34\t7126.5\t9607.21\t7496.34\t2590.08\t3386.61\t1306.67\t2253.64\t8358.76\t12554.98\t15110.48\t15702.85\t11293.88\t9335.59\t8520.23\t11745.11\t9968.7\t13071.81\t14839.87\t9383.9\t14817.83\t6391.49\t12950.4\t7933.23\t14545.8\t7172.25\t10370.07\t5788.85\t8762.2\t12466.91\t9772.54\t12436.37\t9893.37\t10482.42\t8716.03\t14147.85\t6218.7\t9623.6\t11210.63\t10233.45\n+A_92_P026747\t.\t.\t.\t.\t.\t.\t.\t.\t144.3\t198.67\t219.5\t259.35\t160.25\t228.43\t.\t.\t268.09\t211.61\t144.5\t178.74\t350.43\t172.76\t160.31\t237.46\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t232.63\t131.54\t246.58\t172.99\t290.96\t274.14\t188.28\t284.71\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t200.62\t240.06\t.\t.\t215.84\t273.68\t.\t.\t.\t.\t.\t.\t292.35\t81.08\t194.56\t131.87\t.\t.\t.\t.\t.\t.\t250.02\t223.97\t95.74\t199.58\t.\t.\t124.48\t271.42\t.\t.\t191.64\t257.01\t.\t.\t.\t.\t170.18\t248.05\t.\t.\t.\t.\n+-stop traits\n+-quit\n+-end\n' |
| b |
| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/input/qtlcart11.inp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/input/qtlcart11.inp Fri Mar 18 05:51:39 2016 -0400 |
| b |
| b'@@ -0,0 +1,691 @@\n+#bycross\n+-SampleSize 100\n+-Cross Ri1\n+-traits 3\n+-otraits 0\n+-missingtrait .\n+-case yes\n+-TranslationTable\n+AA\t2\tA\n+Aa\t1\t*1\n+aa\t0\tB\n+A-\t12\t*2\n+a-\t10\t*3\n+--\t-1\t-\n+-start markers\n+phi056 A A B B A B B A A A B A B A A A A A A A A A B A \n+B B A B - B B A B B - - A B A B A - - A B A A A A B A A A - B A B B - \n+A - B B B B A B A B A B - - A B A B A - B A A A A B A A B A B A A B A \n+B A B A A B \n+bnl5.62 A A - B A B B A B A B A B B A A A A A A A A B A \n+B A - B - A A A B A - A A B A B A B A A B A A A - B A A A B B A B B - \n+A A B B B B A B A B A A A - A B A B B A B A A - A B A A B A B B A B A \n+B A B A A B \n+umc1041 A A B B A A B A B B A B B A - A B A A A A B B A \n+A A B B - A A A B A B B B B B A - B A A B A A A - A A B - - B A B B B \n+A A B A B A A B A B A A A B A B A B A A B A - A A B A A B A B A A A A \n+B A B B A B \n+umc157a A A B A B A B A A B B - B A A A B - B A A A A A \n+A B B B - A A A B A A A B B A A B B B A A - B A A B A B A A B A A B B \n+A A B A B A A B B A A A A B A B B A B A A A A B A A B A B A B B A B A \n+B A B B B B \n+bnlg1178 A A A A B A B A A B B - B B A A B B B A A B A A \n+A B B B B A A A B A A A B B A A B B B A A - B A B - A B - A A - A B - \n+A A B A A A A B A A A A B B A - A A B B A A A B A A B - B - B B A B A \n+B A B B B B \n+bnlg1429 A A A A B A B A A B B B B B A A B - B A A B A A \n+A B B B B A A A B A A A B B A A B A B A A - B A B B A B - - A A B B - \n+B A B A A A A B A A A A A B A - A A B A A A A B A A B A B A A B A B A \n+B A B B B B \n+bnlg1627 A A A A B B A A B B A B B A A A B B B A A B A A \n+A B - B B A A A B A A A B B A A B A B A A - B A B B A B B - - A B B - \n+A A B A A A A B A B A A A B A B A A B A A A A B A A B A A A A B A B A \n+A A B B B B \n+umc11a A A - A B B B A B B A A B A A B B B B A A A - B \n+A B B B A B A A B B B A B B B A B A B A A B B A B - B B A B A B A B B \n+A A B B A A A B - B A A A B A B B A B A B - A B A A B B A B B - A B A \n+B A B B B B \n+bnlg439 A A A A B B A A B B A A - A A B B B B A A A B B \n+A B A B A A A A B B B A B B B B A A B A A B A B B - - B A B A B A B B \n+A B B A A A A B - B B A B B A - 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A B A A B B B A A - A A A - B A - B B A - B B A B B \n+A B - A A A A - B A A B A B A B A B B A - B A B A A - B B B A - B - A \n+A A B B A B \n+umc1122 A B A A B A B A B B A B B B A A A B A B A B B A \n+B B A B B B A A B A B A A B B B A A B A A A B B A B B A A A B A A B A \n+A B A A A A B A B A B B A B A B A B B A A A B B A B B B B B B B B B B \n+A A B A A B \n+Bnlg615_U A A B A B B A A B A A B A B A B A B A A A B B B \n+B A A A B A A B B B B A A B B B A A B A A B B B A B B A A - B - A B A \n+A A B A B A B B B A B B A B - B A B B A A A B A A B B B A B B B B B B \n+A A B A A B \n+umc1128 A B B A B B B B B B B A A B A B A B A B A B B A \n+A A B A B A A B B B B A A B B B A A B A A B B B '..b'A B B A B A A B B B A B A - A B A A B A B B A B B \n+A B A A A B A A B A B A B - A B A B A B A B A - A A B A B A B B B B - \n+A B B A A A \n+umc1115 A B B B A B A A A B B B A B A A A A B A A A A B \n+B A A A B B B A A B A B - A B A A B - B A B A A A A A A B A A A A A B \n+A B A A B A A A B A B A A A B B A A B A B A A A A A A A B A A A A A A \n+B B B A A A \n+npi232a A B A B A B B A A B B B A B A A A A A A A A A B \n+B A A A B B B A A B A B B A B B A B A B A A A B A A A A B A A A A A B \n+A B A A A A A A B A B A A A B B A A A A A A A A A A A A A A A A A A A \n+B A B A A A \n+umc44a A B A B A B B A A B B B B B A A A A A A A A A B \n+B A B A B A B A A - B B A A B A A B A B A A A A - A - A B A B A A - B \n+A B A A A A A B B A A A A A A B A A A A A A A A A A A A A - B A A A A \n+B B B A A A \n+umc182 B B A B A B B A A B B B B B A A B A A B B A A B \n+A A B A B A B A B B B B B A B A A B A B A - A A B A B A B A B A A - B \n+A B B A A B A B B A A A A A A B A B A A A B A A A A A B A B B B A A A \n+B B B A B A \n+bnlg236 B A A B A B A A A B B A B B A A A A A B B A A B \n+A A B A B B B A B B B B B A B A A B A B A A A B B A B A B B B A A A B \n+A B B A A A A B B A A A A A A B A B A A A B A B A - A B A B B A A A A \n+A B B A B A \n+bnl7.49a B A - B B A A - A A A - A B A A A A A B B A A B \n+A - B A B B - A A B B B - B B A A A A A A - A B B A B A B B B A A - B \n+B A A A A B A A B A B A A A A B A B A A B - A - A B - B - B B - A A A \n+A B B A B A \n+bnlg1450 A A A B A B A A A B - A A B A B A A A B A A A B \n+A B B - A B B A A B B B B B B A A B A A A - A A B A B A B A B A B - B \n+B B A B A B A A - A B A B A B B A B A B B A A B A A A B A B B A B A A \n+A B A A B A \n+umc1038 A A A B B B A B B B B A B A A B A A A B A B A B \n+A B B B A A A A B A B B B - A A - A - B A B B A B B B A B A B A B - B \n+B B B B A B A B A A B A - A B B B B A B A A B B A A A B - B A B B B A \n+A B A A B - \n+-stop markers\n+-start traits\n+A_92_P025313\t10457.22\t10490.57\t9798.33\t9999.53\t8798.36\t7046.18\t6892.34\t10160.6\t7689.89\t8663.87\t9871.88\t10921.34\t9937.08\t12308.57\t8465.21\t7782.51\t9853.2\t11761.78\t10664.15\t13663.05\t18169.19\t14191.86\t12872.1\t15384.53\t10366.49\t11288.81\t39077.24\t6830.99\t9329.34\t10502.21\t12941.67\t9304.69\t5467.51\t6509.71\t9044.5\t9423.92\t11548.33\t7461.03\t9925.06\t10487.97\t13135.98\t12507.83\t1190.45\t1964.29\t10034.9\t8646.24\t9376.45\t10389.52\t6946\t6172.69\t8851.5\t9664.21\t7940.42\t11583.32\t10464.79\t9380.09\t8545.25\t4967.88\t9473.92\t8342.41\t12659.24\t7194.44\t9445.58\t7840.91\t3012.88\t4041.85\t2083.2\t3165.87\t15313.36\t12466.35\t13236.85\t11928.09\t7982.48\t7815.43\t11390.63\t10484.23\t6639.95\t13789.98\t13726.83\t10100.88\t7828.36\t11545.92\t8857.03\t11624.33\t8702.63\t10032.24\t11863.16\t12375.05\t7595.19\t5791.91\t10570.5\t9665.36\t10885.21\t10728.97\t7344.52\t10813.21\t10038.34\t10662.44\t11515.55\t8239.59\n+A_92_P024994\t1661.57\t890.2\t.\t.\t.\t.\t.\t.\t1235.16\t737.54\t739.79\t871.79\t.\t.\t.\t.\t590.54\t847.27\t1507.82\t1619.47\t.\t.\t703.22\t1254.11\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t1559.07\t1343.21\t.\t.\t260.3\t145.61\t.\t.\t.\t.\t306.29\t1440.81\t2182.25\t529.42\t128.08\t768.29\t1135.16\t367.41\t.\t.\t.\t.\t1356.92\t678.78\t.\t.\t.\t.\t385\t466.27\t.\t.\t.\t.\t.\t.\t825.23\t1418.45\t3143.63\t1082.34\t.\t.\t489.56\t618.88\t.\t.\t.\t.\t1101.1\t469.43\t1698.87\t110.84\t221.44\t1494.81\t.\t.\t.\t.\t.\t.\t.\t.\n+A_92_P024836\t481.46\t613.58\t361.73\t605.93\t699.45\t545.81\t485.21\t437.71\t599.14\t521.37\t380.74\t676.56\t557.87\t616.06\t796.97\t904.77\t836.18\t1078.32\t1450.43\t1577.96\t1547.2\t1162.48\t1269.94\t1511.58\t.\t.\t633.5\t662.52\t700.95\t930.87\t.\t.\t554.69\t612.15\t908.32\t547.76\t967.95\t646.22\t675.51\t829.06\t1533.69\t973.73\t151.85\t144.08\t964.56\t1023.46\t1049.41\t845.08\t497.94\t579.33\t703.34\t710.52\t558.92\t721.75\t616.07\t670.8\t449.2\t461.99\t540.43\t591.78\t608.1\t553.46\t572.76\t466.38\t334.14\t285.21\t.\t.\t798.9\t1147.29\t1080.27\t679.76\t539.77\t464.73\t659.19\t1099.79\t563.94\t756.32\t513.76\t744.7\t542.71\t763.01\t672.83\t662.44\t565.08\t722.87\t691.77\t734.88\t603.75\t493.19\t582.62\t722.64\t662.31\t585.01\t546.61\t655.85\t504.25\t578.91\t669.51\t922.93\n+-stop traits\n+-quit\n+-end\n' |
| b |
| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/input/qtlcart12.inp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/input/qtlcart12.inp Fri Mar 18 05:51:39 2016 -0400 |
| b |
| b'@@ -0,0 +1,691 @@\n+#bycross\n+-SampleSize 100\n+-Cross Ri1\n+-traits 3\n+-otraits 0\n+-missingtrait .\n+-case yes\n+-TranslationTable\n+AA\t2\tA\n+Aa\t1\t*1\n+aa\t0\tB\n+A-\t12\t*2\n+a-\t10\t*3\n+--\t-1\t-\n+-start markers\n+phi056 A A B B A B B A A A B A B A A A A A A A A A B A \n+B B A B - B B A B B - - A B A B A - - A B A A A A B A A A - B A B B - \n+A - B B B B A B A B A B - - A B A B A - B A A A A B A A B A B A A B A \n+B A B A A B \n+bnl5.62 A A - B A B B A B A B A B B A A A A A A A A B A \n+B A - B - A A A B A - A A B A B A B A A B A A A - B A A A B B A B B - \n+A A B B B B A B A B A A A - A B A B B A B A A - A B A A B A B B A B A \n+B A B A A B \n+umc1041 A A B B A A B A B B A B B A - A B A A A A B B A \n+A A B B - A A A B A B B B B B A - B A A B A A A - A A B - - B A B B B \n+A A B A B A A B A B A A A B A B A B A A B A - A A B A A B A B A A A A \n+B A B B A B \n+umc157a A A B A B A B A A B B - B A A A B - B A A A A A \n+A B B B - A A A B A A A B B A A B B B A A - B A A B A B A A B A A B B \n+A A B A B A A B B A A A A B A B B A B A A A A B A A B A B A B B A B A \n+B A B B B B \n+bnlg1178 A A A A B A B A A B B - B B A A B B B A A B A A \n+A B B B B A A A B A A A B B A A B B B A A - B A B - A B - A A - A B - \n+A A B A A A A B A A A A B B A - A A B B A A A B A A B - B - B B A B A \n+B A B B B B \n+bnlg1429 A A A A B A B A A B B B B B A A B - B A A B A A \n+A B B B B A A A B A A A B B A A B A B A A - B A B B A B - - A A B B - \n+B A B A A A A B A A A A A B A - A A B A A A A B A A B A B A A B A B A \n+B A B B B B \n+bnlg1627 A A A A B B A A B B A B B A A A B B B A A B A A \n+A B - B B A A A B A A A B B A A B A B A A - B A B B A B B - - A B B - \n+A A B A A A A B A B A A A B A B A A B A A A A B A A B A A A A B A B A \n+A A B B B B \n+umc11a A A - A B B B A B B A A B A A B B B B A A A - B \n+A B B B A B A A B B B A B B B A B A B A A B B A B - B B A B A B A B B \n+A A B B A A A B - B A A A B A B B A B A B - A B A A B B A B B - A B A \n+B A B B B B \n+bnlg439 A A A A B B A A B B A A - A A B B B B A A A B B \n+A B A B A A A A B B B A B B B B A A B A A B A B B - - B A B A B A B B \n+A B B A A A A B - B B A B B A - B B B B A A A B A - B A B B B - B - A \n+A A B B B B \n+bnlg2238 A A A - B B A A B B A B A A A B B A A A A A A B \n+A B A B A A A A B B B A A B B A A A - A A B A B B A A B A B A B - B B \n+A B B B A A A B B B B A A B A B B B B A A - A A A A A A A A A A B A A \n+A A - B B B \n+Bnlg1811_U A A A B B A A B B B B B A A A A B A A A A A A B \n+A B A B B B A A B B A A A B B A B A A A B B B B A A B B A B A B A B B \n+A B B B A A A B B B B A A B A B B B B A A A A B - B A B B B A A B A A \n+A A B B A B \n+bnlg2086 A B A A A A A A B B B B A A B - B A A B A A A B \n+A B A B B B A A B A B A A B B B B A A B B - A B B A B B A B B B A B B \n+B B B B A A A B B B A A A B B B - B B A - A A B B A A B B B A A B A A \n+A A A B A B \n+csu61b B B - A B A A A B B B B A B A - B B B B - B A B \n+B A A B B A A A B A B A A B B B B A - B A A - B - B B B A B B B A B B \n+A B B A A A A B B B A B A B A B - B B A - - A B A A - B B B A - B - A \n+A A B B A B \n+bnlg1057 B B A A A A B A B B B B A B A - B B A B B B B B \n+A B A B B A A A - A B A A B B B A A - A A A - B A - B B A - B B A B B \n+A B - A A A A - B A A B A B A B A B B A - B A B A A - B B B A - B - A \n+A A B B A B \n+umc1122 A B A A B A B A B B A B B B A A A B A B A B B A \n+B B A B B B A A B A B A A B B B A A B A A A B B A B B A A A B A A B A \n+A B A A A A B A B A B B A B A B A B B A A A B B A B B B B B B B B B B \n+A A B A A B \n+Bnlg615_U A A B A B B A A B A A B A B A B A B A A A B B B \n+B A A A B A A B B B B A A B B B A A B A A B B B A B B A A - B - A B A \n+A A B A B A B B B A B B A B - B A B B A A A B A A B B B A B B B B B B \n+A A B A A B \n+umc1128 A B B A B B B B B B B A A B A B A B A B A B B A \n+A A B A B A A B B B B A A B B B A A B A A B B B '..b'B A A A A A B \n+A B A A B A A A B A B A A A B B A A B A B A A A A A A A B A A A A A A \n+B B B A A A \n+npi232a A B A B A B B A A B B B A B A A A A A A A A A B \n+B A A A B B B A A B A B B A B B A B A B A A A B A A A A B A A A A A B \n+A B A A A A A A B A B A A A B B A A A A A A A A A A A A A A A A A A A \n+B A B A A A \n+umc44a A B A B A B B A A B B B B B A A A A A A A A A B \n+B A B A B A B A A - B B A A B A A B A B A A A A - A - A B A B A A - B \n+A B A A A A A B B A A A A A A B A A A A A A A A A A A A A - B A A A A \n+B B B A A A \n+umc182 B B A B A B B A A B B B B B A A B A A B B A A B \n+A A B A B A B A B B B B B A B A A B A B A - A A B A B A B A B A A - B \n+A B B A A B A B B A A A A A A B A B A A A B A A A A A B A B B B A A A \n+B B B A B A \n+bnlg236 B A A B A B A A A B B A B B A A A A A B B A A B \n+A A B A B B B A B B B B B A B A A B A B A A A B B A B A B B B A A A B \n+A B B A A A A B B A A A A A A B A B A A A B A B A - A B A B B A A A A \n+A B B A B A \n+bnl7.49a B A - B B A A - A A A - A B A A A A A B B A A B \n+A - B A B B - A A B B B - B B A A A A A A - A B B A B A B B B A A - B \n+B A A A A B A A B A B A A A A B A B A A B - A - A B - B - B B - A A A \n+A B B A B A \n+bnlg1450 A A A B A B A A A B - A A B A B A A A B A A A B \n+A B B - A B B A A B B B B B B A A B A A A - A A B A B A B A B A B - B \n+B B A B A B A A - A B A B A B B A B A B B A A B A A A B A B B A B A A \n+A B A A B A \n+umc1038 A A A B B B A B B B B A B A A B A A A B A B A B \n+A B B B A A A A B A B B B - A A - A - B A B B A B B B A B A B A B - B \n+B B B B A B A B A A B A - A B B B B A B A A B B A A A B - B A B B B A \n+A B A A B - \n+-stop markers\n+-start traits\n+A_92_P024516\t2374.49\t1682.01\t1427.07\t1999.71\t1630.27\t2664.74\t1628.35\t1422.27\t1900.26\t1512.65\t2183.92\t2652.78\t1815.78\t1673.05\t2572.15\t2448.69\t765.92\t854.29\t1194.06\t1411.72\t1852.99\t2225.45\t1417.63\t1441.01\t1605.15\t1936.45\t1739.53\t2999.07\t1581.6\t1849.75\t1879.79\t2024.83\t1112.46\t2026.72\t2257.62\t1966.16\t1692.35\t3342.29\t1584.6\t2017.57\t1787.54\t1442.35\t464.2\t260.26\t1884.85\t1534.1\t3179.99\t2131.98\t1833.85\t2358.95\t3318.18\t2073.31\t1944.94\t1882.74\t2213.02\t2357.4\t1993.24\t1613.1\t2013.31\t2073.9\t1706.7\t1546.15\t2910.24\t2014.72\t890.58\t878.79\t633.41\t650.33\t1608.84\t1698.46\t1661.94\t1750.84\t1453.07\t2191.43\t1606.12\t2132.88\t2905.1\t1875.54\t1774.13\t2207.78\t2809.76\t1920.85\t3360.32\t2995.68\t3302.03\t1952.98\t2217.18\t2446.22\t2387.25\t1836.56\t2305.1\t1995.68\t2434.19\t2168.51\t2552.98\t1964.36\t1568.81\t2046\t1996.65\t2119.35\n+A_92_P023713\t1629.27\t2895.05\t2216.4\t1907.1\t1802.3\t2302.55\t1758.87\t2480.73\t1416.59\t1757.42\t1538.59\t2307.17\t2017.87\t2023.68\t1431.99\t1470.15\t2836.85\t1812.73\t2765.48\t2648.37\t2636.53\t3907.38\t1935.96\t3235.03\t1908.81\t2307.84\t2402.94\t2752.51\t2020.57\t2619.68\t2067.28\t1464.7\t1292.05\t1406.19\t1955.99\t1593.56\t2830.08\t1718.88\t1836.98\t3754.56\t2910.75\t3332\t.\t.\t1893.45\t2415.97\t3146.16\t1748.64\t2157.51\t1694.66\t2023.09\t3166.39\t1940.19\t2597.11\t2137.94\t1980.19\t1376.29\t1846.62\t2375.53\t1443.82\t2373.37\t2663.96\t2140.55\t1940.27\t979.82\t1127.44\t1402.83\t949.55\t2777.32\t2776.66\t2100.56\t2367.84\t1192.96\t1481.44\t3130.04\t2429.13\t1105.62\t1624.9\t2554.63\t1960.21\t1145.84\t2646.1\t2239.94\t1484.2\t1209.81\t1578.74\t2265.28\t3493.69\t1805.45\t872.41\t2018.76\t2638.71\t2150.22\t1593.16\t2302.28\t1981.39\t1518.37\t2322.63\t2211.65\t2359.99\n+A_92_P023551\t.\t.\t.\t.\t1090.96\t1145.06\t439.02\t224.17\t515.94\t1162.55\t1044.6\t548.93\t688.81\t635.97\t520.49\t703.78\t781.66\t1566.77\t537.3\t815.3\t1631.7\t970.06\t501.04\t668.08\t911.57\t621.11\t730.86\t299\t.\t.\t654.07\t519.57\t778.22\t810.82\t696.22\t343.94\t697.98\t212.5\t1002.96\t503.52\t1333.03\t515.75\t.\t.\t1076.4\t1567.58\t616.47\t785.82\t.\t.\t261.33\t687.36\t866.14\t1001.13\t587.45\t538.58\t770.36\t287.08\t449.35\t536.81\t532.29\t1404.07\t591.91\t1605.42\t336.76\t252.77\t.\t.\t676.45\t250.53\t440.8\t314.18\t780.6\t285.52\t530.62\t928.44\t169.52\t1011.42\t672.66\t499.44\t155.25\t512.52\t237.48\t754.45\t.\t.\t558.12\t922.48\t352.06\t959.28\t214.87\t568.46\t198.96\t1135.89\t353.21\t646.82\t259.08\t1022.22\t1005.88\t907.6\n+-stop traits\n+-quit\n+-end\n' |
| b |
| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/input/qtlcart13.inp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/input/qtlcart13.inp Fri Mar 18 05:51:39 2016 -0400 |
| b |
| b'@@ -0,0 +1,691 @@\n+#bycross\n+-SampleSize 100\n+-Cross Ri1\n+-traits 3\n+-otraits 0\n+-missingtrait .\n+-case yes\n+-TranslationTable\n+AA\t2\tA\n+Aa\t1\t*1\n+aa\t0\tB\n+A-\t12\t*2\n+a-\t10\t*3\n+--\t-1\t-\n+-start markers\n+phi056 A A B B A B B A A A B A B A A A A A A A A A B A \n+B B A B - B B A B B - - A B A B A - - A B A A A A B A A A - B A B B - \n+A - B B B B A B A B A B - - A B A B A - B A A A A B A A B A B A A B A \n+B A B A A B \n+bnl5.62 A A - B A B B A B A B A B B A A A A A A A A B A \n+B A - B - A A A B A - A A B A B A B A A B A A A - B A A A B B A B B - \n+A A B B B B A B A B A A A - A B A B B A B A A - A B A A B A B B A B A \n+B A B A A B \n+umc1041 A A B B A A B A B B A B B A - A B A A A A B B A \n+A A B B - A A A B A B B B B B A - B A A B A A A - A A B - - B A B B B \n+A A B A B A A B A B A A A B A B A B A A B A - A A B A A B A B A A A A \n+B A B B A B \n+umc157a A A B A B A B A A B B - B A A A B - B A A A A A \n+A B B B - A A A B A A A B B A A B B B A A - B A A B A B A A B A A B B \n+A A B A B A A B B A A A A B A B B A B A A A A B A A B A B A B B A B A \n+B A B B B B \n+bnlg1178 A A A A B A B A A B B - B B A A B B B A A B A A \n+A B B B B A A A B A A A B B A A B B B A A - B A B - A B - A A - A B - \n+A A B A A A A B A A A A B B A - A A B B A A A B A A B - B - B B A B A \n+B A B B B B \n+bnlg1429 A A A A B A B A A B B B B B A A B - B A A B A A \n+A B B B B A A A B A A A B B A A B A B A A - B A B B A B - - A A B B - \n+B A B A A A A B A A A A A B A - A A B A A A A B A A B A B A A B A B A \n+B A B B B B \n+bnlg1627 A A A A B B A A B B A B B A A A B B B A A B A A \n+A B - B B A A A B A A A B B A A B A B A A - B A B B A B B - - A B B - \n+A A B A A A A B A B A A A B A B A A B A A A A B A A B A A A A B A B A \n+A A B B B B \n+umc11a A A - A B B B A B B A A B A A B B B B A A A - B \n+A B B B A B A A B B B A B B B A B A B A A B B A B - B B A B A B A B B \n+A A B B A A A B - B A A A B A B B A B A B - A B A A B B A B B - A B A \n+B A B B B B \n+bnlg439 A A A A B B A A B B A A - A A B B B B A A A B B \n+A B A B A A A A B B B A B B B B A A B A A B A B B - - B A B A B A B B \n+A B B A A A A B - B B A B B A - B B B B A A A B A - B A B B B - B - A \n+A A B B B B \n+bnlg2238 A A A - B B A A B B A B A A A B B A A A A A A B \n+A B A B A A A A B B B A A B B A A A - A A B A B B A A B A B A B - B B \n+A B B B A A A B B B B A A B A B B B B A A - A A A A A A A A A A B A A \n+A A - B B B \n+Bnlg1811_U A A A B B A A B B B B B A A A A B A A A A A A B \n+A B A B B B A A B B A A A B B A B A A A B B B B A A B B A B A B A B B \n+A B B B A A A B B B B A A B A B B B B A A A A B - B A B B B A A B A A \n+A A B B A B \n+bnlg2086 A B A A A A A A B B B B A A B - B A A B A A A B \n+A B A B B B A A B A B A A B B B B A A B B - A B B A B B A B B B A B B \n+B B B B A A A B B B A A A B B B - B B A - A A B B A A B B B A A B A A \n+A A A B A B \n+csu61b B B - A B A A A B B B B A B A - B B B B - B A B \n+B A A B B A A A B A B A A B B B B A - B A A - B - B B B A B B B A B B \n+A B B A A A A B B B A B A B A B - B B A - - A B A A - B B B A - B - A \n+A A B B A B \n+bnlg1057 B B A A A A B A B B B B A B A - B B A B B B B B \n+A B A B B A A A - A B A A B B B A A - A A A - B A - B B A - B B A B B \n+A B - A A A A - B A A B A B A B A B B A - B A B A A - B B B A - B - A \n+A A B B A B \n+umc1122 A B A A B A B A B B A B B B A A A B A B A B B A \n+B B A B B B A A B A B A A B B B A A B A A A B B A B B A A A B A A B A \n+A B A A A A B A B A B B A B A B A B B A A A B B A B B B B B B B B B B \n+A A B A A B \n+Bnlg615_U A A B A B B A A B A A B A B A B A B A A A B B B \n+B A A A B A A B B B B A A B B B A A B A A B B B A B B A A - B - A B A \n+A A B A B A B B B A B B A B - B A B B A A A B A A B B B A B B B B B B \n+A A B A A B \n+umc1128 A B B A B B B B B B B A A B A B A B A B A B B A \n+A A B A B A A B B B B A A B B B A A B A A B B B '..b'B A B B A B A B A A A B B B A B - A B \n+A A A B B A B A A B A B B A - A A B B B A B A B A B A B B - A B A B B \n+A B A A A A A A - B B A B A A B A B A B B B A A A A B A B A B B B B A \n+A B B B A A \n+bnlg1079 B B A B B B A A B A B A A A A A A B B A B A A B \n+A A A B B B B A A B A B B A B A A B B B A B A - A B A A B A B B A B B \n+A B A A A B A A B A B A B - A B A B A B A B A - A A B A B A B B B B - \n+A B B A A A \n+umc1115 A B B B A B A A A B B B A B A A A A B A A A A B \n+B A A A B B B A A B A B - A B A A B - B A B A A A A A A B A A A A A B \n+A B A A B A A A B A B A A A B B A A B A B A A A A A A A B A A A A A A \n+B B B A A A \n+npi232a A B A B A B B A A B B B A B A A A A A A A A A B \n+B A A A B B B A A B A B B A B B A B A B A A A B A A A A B A A A A A B \n+A B A A A A A A B A B A A A B B A A A A A A A A A A A A A A A A A A A \n+B A B A A A \n+umc44a A B A B A B B A A B B B B B A A A A A A A A A B \n+B A B A B A B A A - B B A A B A A B A B A A A A - A - A B A B A A - B \n+A B A A A A A B B A A A A A A B A A A A A A A A A A A A A - B A A A A \n+B B B A A A \n+umc182 B B A B A B B A A B B B B B A A B A A B B A A B \n+A A B A B A B A B B B B B A B A A B A B A - A A B A B A B A B A A - B \n+A B B A A B A B B A A A A A A B A B A A A B A A A A A B A B B B A A A \n+B B B A B A \n+bnlg236 B A A B A B A A A B B A B B A A A A A B B A A B \n+A A B A B B B A B B B B B A B A A B A B A A A B B A B A B B B A A A B \n+A B B A A A A B B A A A A A A B A B A A A B A B A - A B A B B A A A A \n+A B B A B A \n+bnl7.49a B A - B B A A - A A A - A B A A A A A B B A A B \n+A - B A B B - A A B B B - B B A A A A A A - A B B A B A B B B A A - B \n+B A A A A B A A B A B A A A A B A B A A B - A - A B - B - B B - A A A \n+A B B A B A \n+bnlg1450 A A A B A B A A A B - A A B A B A A A B A A A B \n+A B B - A B B A A B B B B B B A A B A A A - A A B A B A B A B A B - B \n+B B A B A B A A - A B A B A B B A B A B B A A B A A A B A B B A B A A \n+A B A A B A \n+umc1038 A A A B B B A B B B B A B A A B A A A B A B A B \n+A B B B A A A A B A B B B - A A - A - B A B B A B B B A B A B A B - B \n+B B B B A B A B A A B A - A B B B B A B A A B B A A A B - B A B B B A \n+A B A A B - \n+-stop markers\n+-start traits\n+A_92_P023394\t355.21\t571.3\t745.58\t552.66\t630.67\t556.2\t628.44\t558.5\t525.14\t640.89\t634.48\t673.26\t479.42\t698.21\t.\t.\t838.8\t852.85\t688.08\t506.74\t1019.54\t778.95\t679.07\t904.35\t587.64\t639.91\t498.6\t402.09\t550.51\t524.52\t512.02\t567.25\t.\t.\t546.07\t513.87\t533.11\t472.07\t569.75\t549.37\t884.33\t769.32\t.\t.\t534.93\t612.56\t414.91\t555.49\t.\t.\t339.01\t729.16\t423.51\t657.36\t394.8\t586.83\t487.81\t476.18\t650.74\t614.17\t574.44\t703.9\t686.84\t703.57\t.\t.\t299.7\t309.57\t637.04\t566.19\t592.38\t661.25\t379.77\t495.71\t548.59\t570.87\t292.82\t641.99\t996.73\t615.73\t218.49\t502.76\t369.97\t577.16\t338.85\t615.03\t533.89\t635.7\t431.65\t679.27\t406.39\t701.03\t401.2\t668.23\t562.33\t538.64\t427.27\t482.88\t693.9\t534.2\n+A_92_P023235\t339.76\t514.77\t525.84\t508.63\t460.93\t446.58\t465.64\t360.23\t397.22\t416.58\t428.52\t555.86\t406.94\t437.64\t413.08\t501.1\t426.91\t398.83\t357.21\t339.62\t786.82\t531.65\t464.99\t470.84\t.\t.\t343.97\t322.55\t.\t.\t.\t.\t.\t.\t330.03\t428.04\t411.1\t278.33\t465.8\t433.35\t404.72\t444.72\t.\t.\t.\t.\t429.72\t580.85\t325.32\t233.97\t312.49\t523.49\t571.09\t403.91\t448.85\t398.31\t386.94\t434.69\t362.26\t537.05\t341.09\t551.61\t406.16\t432.2\t168.77\t202.73\t319.56\t294.91\t446.38\t292.88\t454.91\t406.64\t502.95\t402.94\t452.69\t487.11\t308.15\t547.9\t498.54\t480.18\t263.62\t381.78\t285.2\t501.07\t360.8\t630.26\t596\t358.38\t384.76\t507.39\t325.09\t459.54\t326.82\t558.89\t474.67\t486.08\t352.13\t430.22\t436.95\t439.26\n+A_92_P023080\t188.68\t185.58\t.\t.\t.\t.\t.\t.\t300.05\t358.4\t.\t.\t352.52\t382.28\t.\t.\t.\t.\t143.14\t137.39\t.\t.\t250.24\t298.07\t.\t.\t372.32\t317.5\t230.58\t445.45\t.\t.\t.\t.\t.\t.\t611.7\t97.72\t.\t.\t327.08\t327.63\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t129.55\t426.21\t346.29\t439.69\t.\t.\t.\t.\t565.12\t130.75\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t297.02\t105.51\t323.92\t124.52\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t384.98\t182.37\t.\t.\t79.66\t329.72\t.\t.\t.\t.\t320.59\t394.5\t.\t.\n+-stop traits\n+-quit\n+-end\n' |
| b |
| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/input/qtlcart14.inp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/input/qtlcart14.inp Fri Mar 18 05:51:39 2016 -0400 |
| b |
| b'@@ -0,0 +1,691 @@\n+#bycross\n+-SampleSize 100\n+-Cross Ri1\n+-traits 3\n+-otraits 0\n+-missingtrait .\n+-case yes\n+-TranslationTable\n+AA\t2\tA\n+Aa\t1\t*1\n+aa\t0\tB\n+A-\t12\t*2\n+a-\t10\t*3\n+--\t-1\t-\n+-start markers\n+phi056 A A B B A B B A A A B A B A A A A A A A A A B A \n+B B A B - B B A B B - - A B A B A - - A B A A A A B A A A - B A B B - \n+A - B B B B A B A B A B - - A B A B A - B A A A A B A A B A B A A B A \n+B A B A A B \n+bnl5.62 A A - B A B B A B A B A B B A A A A A A A A B A \n+B A - B - A A A B A - A A B A B A B A A B A A A - B A A A B B A B B - \n+A A B B B B A B A B A A A - A B A B B A B A A - A B A A B A B B A B A \n+B A B A A B \n+umc1041 A A B B A A B A B B A B B A - A B A A A A B B A \n+A A B B - A A A B A B B B B B A - B A A B A A A - A A B - - B A B B B \n+A A B A B A A B A B A A A B A B A B A A B A - A A B A A B A B A A A A \n+B A B B A B \n+umc157a A A B A B A B A A B B - B A A A B - B A A A A A \n+A B B B - A A A B A A A B B A A B B B A A - B A A B A B A A B A A B B \n+A A B A B A A B B A A A A B A B B A B A A A A B A A B A B A B B A B A \n+B A B B B B \n+bnlg1178 A A A A B A B A A B B - B B A A B B B A A B A A \n+A B B B B A A A B A A A B B A A B B B A A - B A B - A B - A A - A B - \n+A A B A A A A B A A A A B B A - A A B B A A A B A A B - B - B B A B A \n+B A B B B B \n+bnlg1429 A A A A B A B A A B B B B B A A B - B A A B A A \n+A B B B B A A A B A A A B B A A B A B A A - B A B B A B - - A A B B - \n+B A B A A A A B A A A A A B A - A A B A A A A B A A B A B A A B A B A \n+B A B B B B \n+bnlg1627 A A A A B B A A B B A B B A A A B B B A A B A A \n+A B - B B A A A B A A A B B A A B A B A A - B A B B A B B - - A B B - \n+A A B A A A A B A B A A A B A B A A B A A A A B A A B A A A A B A B A \n+A A B B B B \n+umc11a A A - A B B B A B B A A B A A B B B B A A A - B \n+A B B B A B A A B B B A B B B A B A B A A B B A B - B B A B A B A B B \n+A A B B A A A B - B A A A B A B B A B A B - A B A A B B A B B - A B A \n+B A B B B B \n+bnlg439 A A A A B B A A B B A A - A A B B B B A A A B B \n+A B A B A A A A B B B A B B B B A A B A A B A B B - - B A B A B A B B \n+A B B A A A A B - B B A B B A - B B B B A A A B A - B A B B B - B - A \n+A A B B B B \n+bnlg2238 A A A - B B A A B B A B A A A B B A A A A A A B \n+A B A B A A A A B B B A A B B A A A - A A B A B B A A B A B A B - B B \n+A B B B A A A B B B B A A B A B B B B A A - A A A A A A A A A A B A A \n+A A - B B B \n+Bnlg1811_U A A A B B A A B B B B B A A A A B A A A A A A B \n+A B A B B B A A B B A A A B B A B A A A B B B B A A B B A B A B A B B \n+A B B B A A A B B B B A A B A B B B B A A A A B - B A B B B A A B A A \n+A A B B A B \n+bnlg2086 A B A A A A A A B B B B A A B - B A A B A A A B \n+A B A B B B A A B A B A A B B B B A A B B - A B B A B B A B B B A B B \n+B B B B A A A B B B A A A B B B - B B A - A A B B A A B B B A A B A A \n+A A A B A B \n+csu61b B B - A B A A A B B B B A B A - B B B B - B A B \n+B A A B B A A A B A B A A B B B B A - B A A - B - B B B A B B B A B B \n+A B B A A A A B B B A B A B A B - B B A - - A B A A - B B B A - B - A \n+A A B B A B \n+bnlg1057 B B A A A A B A B B B B A B A - B B A B B B B B \n+A B A B B A A A - A B A A B B B A A - A A A - B A - B B A - B B A B B \n+A B - A A A A - B A A B A B A B A B B A - B A B A A - B B B A - B - A \n+A A B B A B \n+umc1122 A B A A B A B A B B A B B B A A A B A B A B B A \n+B B A B B B A A B A B A A B B B A A B A A A B B A B B A A A B A A B A \n+A B A A A A B A B A B B A B A B A B B A A A B B A B B B B B B B B B B \n+A A B A A B \n+Bnlg615_U A A B A B B A A B A A B A B A B A B A A A B B B \n+B A A A B A A B B B B A A B B B A A B A A B B B A B B A A - B - A B A \n+A A B A B A B B B A B B A B - B A B B A A A B A A B B B A B B B B B B \n+A A B A A B \n+umc1128 A B B A B B B B B B B A A B A B A B A B A B B A \n+A A B A B A A B B B B A A B B B A A B A A B B B '..b'A B A B A A A A A A A B A A A A A A \n+B B B A A A \n+npi232a A B A B A B B A A B B B A B A A A A A A A A A B \n+B A A A B B B A A B A B B A B B A B A B A A A B A A A A B A A A A A B \n+A B A A A A A A B A B A A A B B A A A A A A A A A A A A A A A A A A A \n+B A B A A A \n+umc44a A B A B A B B A A B B B B B A A A A A A A A A B \n+B A B A B A B A A - B B A A B A A B A B A A A A - A - A B A B A A - B \n+A B A A A A A B B A A A A A A B A A A A A A A A A A A A A - B A A A A \n+B B B A A A \n+umc182 B B A B A B B A A B B B B B A A B A A B B A A B \n+A A B A B A B A B B B B B A B A A B A B A - A A B A B A B A B A A - B \n+A B B A A B A B B A A A A A A B A B A A A B A A A A A B A B B B A A A \n+B B B A B A \n+bnlg236 B A A B A B A A A B B A B B A A A A A B B A A B \n+A A B A B B B A B B B B B A B A A B A B A A A B B A B A B B B A A A B \n+A B B A A A A B B A A A A A A B A B A A A B A B A - A B A B B A A A A \n+A B B A B A \n+bnl7.49a B A - B B A A - A A A - A B A A A A A B B A A B \n+A - B A B B - A A B B B - B B A A A A A A - A B B A B A B B B A A - B \n+B A A A A B A A B A B A A A A B A B A A B - A - A B - B - B B - A A A \n+A B B A B A \n+bnlg1450 A A A B A B A A A B - A A B A B A A A B A A A B \n+A B B - A B B A A B B B B B B A A B A A A - A A B A B A B A B A B - B \n+B B A B A B A A - A B A B A B B A B A B B A A B A A A B A B B A B A A \n+A B A A B A \n+umc1038 A A A B B B A B B B B A B A A B A A A B A B A B \n+A B B B A A A A B A B B B - A A - A - B A B B A B B B A B A B A B - B \n+B B B B A B A B A A B A - A B B B B A B A A B B A A A B - B A B B B A \n+A B A A B - \n+-stop markers\n+-start traits\n+A_92_P022918\t2421.67\t4395.38\t2614.36\t4278.06\t3012.67\t2222.33\t2950.03\t2432.77\t2607.35\t3892.95\t2601.79\t2193.37\t4266.99\t2538.98\t3307.74\t1675.45\t2867.06\t5765.85\t3172.23\t6172.48\t3925.27\t6654\t5152.83\t5423.15\t4434.42\t4536.68\t2414.96\t4157.63\t2375.48\t3375.12\t2036.47\t2092.63\t3367.44\t1938.1\t2272.71\t2413.42\t2328.39\t2861.56\t4299.35\t3745.4\t6574.11\t5645.94\t1290.46\t1154.53\t2258.77\t1989.24\t2678.83\t3708.59\t3486.09\t2219.29\t3114.54\t2729.31\t4692.42\t2884.9\t3523.39\t4703.4\t2181.14\t1969.13\t4500.85\t2178.74\t3728.38\t4484.14\t3465.31\t2499.03\t1288.73\t1300.43\t1581.55\t1745.34\t3637.32\t5448.82\t2548.03\t2872.89\t3798.05\t2034.41\t2365.31\t2543.79\t2167.64\t4821.97\t3065.4\t2358.07\t2334.12\t2144.6\t4078.15\t4753.89\t2333.36\t2438.07\t4191.12\t2169.1\t3971.19\t3016.13\t2652.88\t2887.55\t2665.57\t2898.75\t3207.77\t4781.41\t4203.19\t4465.5\t4874.93\t4407.9\n+A_92_P022755\t16655.23\t6033.53\t5205.62\t5329.5\t12963.79\t1195.8\t1824.44\t826.59\t4560.89\t3631.27\t1714.78\t6046.95\t7284.27\t2466.14\t14394.34\t10942.85\t1943.6\t3287.46\t2269.85\t17126.03\t13377.01\t779.19\t3622.15\t6109.8\t1117.55\t3559\t10313.57\t3198.16\t11031.13\t2706.78\t3146.87\t14162.18\t2326.32\t11860.84\t6328.68\t17767.19\t3785.96\t8858.56\t15823.92\t2929.37\t2552.87\t2476.64\t4274.2\t1035.33\t4082.83\t9470.23\t3468.44\t6086.08\t2967.03\t6828.88\t12303.91\t1119.43\t5197.48\t2295.27\t4720.12\t6561.57\t1304.39\t1860.98\t4025.5\t15728.94\t8455.4\t1521.11\t9774.11\t5495.46\t2906.71\t1333.11\t.\t.\t2604.29\t4034.36\t6574.96\t4541.31\t5143.17\t3116.19\t7152.94\t7434.2\t26562.24\t2784.86\t5342.14\t8879.31\t16436.39\t907.14\t13915.78\t11431.35\t22808.64\t14638.76\t3071.98\t2811.69\t9718.19\t3789.27\t11168.8\t1241.94\t10523.5\t9257.08\t4303.29\t10028.53\t2580.39\t957.91\t5626.63\t8370.38\n+A_92_P022592\t1039.19\t591.49\t495.27\t701.88\t430.1\t364.08\t421.39\t678.21\t428.33\t435.18\t502.21\t388.61\t543.11\t509.17\t.\t.\t549.74\t466.69\t747.79\t584.13\t702.78\t1069.44\t586.04\t440.54\t387.62\t528.94\t515.53\t843.17\t475.9\t490.47\t442.47\t555.36\t.\t.\t633.77\t542.61\t691.17\t870.78\t501.53\t442.14\t585.16\t577.68\t487.25\t323.67\t.\t.\t596.75\t454.76\t409.9\t528.37\t550.57\t544.95\t381.66\t580.13\t554.62\t509.07\t378.61\t358.43\t425.42\t430.39\t635.36\t442.07\t677.75\t424.13\t361.91\t246.79\t.\t.\t507.01\t789.71\t437.09\t800.01\t365.67\t425.25\t416.97\t407.24\t558.77\t437.17\t594.67\t407.06\t750.74\t561.2\t984.8\t404.09\t759.66\t333.76\t659.14\t555.24\t746.54\t388.53\t671.64\t720.25\t792.91\t334.63\t563.99\t412.09\t639.39\t439.91\t579.05\t485.46\n+-stop traits\n+-quit\n+-end\n' |
| b |
| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/input/qtlcart15.inp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/input/qtlcart15.inp Fri Mar 18 05:51:39 2016 -0400 |
| b |
| b'@@ -0,0 +1,691 @@\n+#bycross\n+-SampleSize 100\n+-Cross Ri1\n+-traits 3\n+-otraits 0\n+-missingtrait .\n+-case yes\n+-TranslationTable\n+AA\t2\tA\n+Aa\t1\t*1\n+aa\t0\tB\n+A-\t12\t*2\n+a-\t10\t*3\n+--\t-1\t-\n+-start markers\n+phi056 A A B B A B B A A A B A B A A A A A A A A A B A \n+B B A B - B B A B B - - A B A B A - - A B A A A A B A A A - B A B B - \n+A - B B B B A B A B A B - - A B A B A - B A A A A B A A B A B A A B A \n+B A B A A B \n+bnl5.62 A A - B A B B A B A B A B B A A A A A A A A B A \n+B A - B - A A A B A - A A B A B A B A A B A A A - B A A A B B A B B - \n+A A B B B B A B A B A A A - A B A B B A B A A - A B A A B A B B A B A \n+B A B A A B \n+umc1041 A A B B A A B A B B A B B A - A B A A A A B B A \n+A A B B - A A A B A B B B B B A - B A A B A A A - A A B - - B A B B B \n+A A B A B A A B A B A A A B A B A B A A B A - A A B A A B A B A A A A \n+B A B B A B \n+umc157a A A B A B A B A A B B - B A A A B - B A A A A A \n+A B B B - A A A B A A A B B A A B B B A A - B A A B A B A A B A A B B \n+A A B A B A A B B A A A A B A B B A B A A A A B A A B A B A B B A B A \n+B A B B B B \n+bnlg1178 A A A A B A B A A B B - B B A A B B B A A B A A \n+A B B B B A A A B A A A B B A A B B B A A - B A B - A B - A A - A B - \n+A A B A A A A B A A A A B B A - A A B B A A A B A A B - B - B B A B A \n+B A B B B B \n+bnlg1429 A A A A B A B A A B B B B B A A B - B A A B A A \n+A B B B B A A A B A A A B B A A B A B A A - B A B B A B - - A A B B - \n+B A B A A A A B A A A A A B A - A A B A A A A B A A B A B A A B A B A \n+B A B B B B \n+bnlg1627 A A A A B B A A B B A B B A A A B B B A A B A A \n+A B - B B A A A B A A A B B A A B A B A A - B A B B A B B - - A B B - \n+A A B A A A A B A B A A A B A B A A B A A A A B A A B A A A A B A B A \n+A A B B B B \n+umc11a A A - A B B B A B B A A B A A B B B B A A A - B \n+A B B B A B A A B B B A B B B A B A B A A B B A B - B B A B A B A B B \n+A A B B A A A B - B A A A B A B B A B A B - A B A A B B A B B - A B A \n+B A B B B B \n+bnlg439 A A A A B B A A B B A A - A A B B B B A A A B B \n+A B A B A A A A B B B A B B B B A A B A A B A B B - - B A B A B A B B \n+A B B A A A A B - B B A B B A - B B B B A A A B A - B A B B B - B - A \n+A A B B B B \n+bnlg2238 A A A - B B A A B B A B A A A B B A A A A A A B \n+A B A B A A A A B B B A A B B A A A - A A B A B B A A B A B A B - B B \n+A B B B A A A B B B B A A B A B B B B A A - A A A A A A A A A A B A A \n+A A - B B B \n+Bnlg1811_U A A A B B A A B B B B B A A A A B A A A A A A B \n+A B A B B B A A B B A A A B B A B A A A B B B B A A B B A B A B A B B \n+A B B B A A A B B B B A A B A B B B B A A A A B - B A B B B A A B A A \n+A A B B A B \n+bnlg2086 A B A A A A A A B B B B A A B - B A A B A A A B \n+A B A B B B A A B A B A A B B B B A A B B - A B B A B B A B B B A B B \n+B B B B A A A B B B A A A B B B - B B A - A A B B A A B B B A A B A A \n+A A A B A B \n+csu61b B B - A B A A A B B B B A B A - B B B B - B A B \n+B A A B B A A A B A B A A B B B B A - B A A - B - B B B A B B B A B B \n+A B B A A A A B B B A B A B A B - B B A - - A B A A - B B B A - B - A \n+A A B B A B \n+bnlg1057 B B A A A A B A B B B B A B A - B B A B B B B B \n+A B A B B A A A - A B A A B B B A A - A A A - B A - B B A - B B A B B \n+A B - A A A A - B A A B A B A B A B B A - B A B A A - B B B A - B - A \n+A A B B A B \n+umc1122 A B A A B A B A B B A B B B A A A B A B A B B A \n+B B A B B B A A B A B A A B B B A A B A A A B B A B B A A A B A A B A \n+A B A A A A B A B A B B A B A B A B B A A A B B A B B B B B B B B B B \n+A A B A A B \n+Bnlg615_U A A B A B B A A B A A B A B A B A B A A A B B B \n+B A A A B A A B B B B A A B B B A A B A A B B B A B B A A - B - A B A \n+A A B A B A B B B A B B A B - B A B B A A A B A A B B B A B B B B B B \n+A A B A A B \n+umc1128 A B B A B B B B B B B A A B A B A B A B A B B A \n+A A B A B A A B B B B A A B B B A A B A A B B B '..b' B \n+B A A A B B B A A B A B B A B B A B A B A A A B A A A A B A A A A A B \n+A B A A A A A A B A B A A A B B A A A A A A A A A A A A A A A A A A A \n+B A B A A A \n+umc44a A B A B A B B A A B B B B B A A A A A A A A A B \n+B A B A B A B A A - B B A A B A A B A B A A A A - A - A B A B A A - B \n+A B A A A A A B B A A A A A A B A A A A A A A A A A A A A - B A A A A \n+B B B A A A \n+umc182 B B A B A B B A A B B B B B A A B A A B B A A B \n+A A B A B A B A B B B B B A B A A B A B A - A A B A B A B A B A A - B \n+A B B A A B A B B A A A A A A B A B A A A B A A A A A B A B B B A A A \n+B B B A B A \n+bnlg236 B A A B A B A A A B B A B B A A A A A B B A A B \n+A A B A B B B A B B B B B A B A A B A B A A A B B A B A B B B A A A B \n+A B B A A A A B B A A A A A A B A B A A A B A B A - A B A B B A A A A \n+A B B A B A \n+bnl7.49a B A - B B A A - A A A - A B A A A A A B B A A B \n+A - B A B B - A A B B B - B B A A A A A A - A B B A B A B B B A A - B \n+B A A A A B A A B A B A A A A B A B A A B - A - A B - B - B B - A A A \n+A B B A B A \n+bnlg1450 A A A B A B A A A B - A A B A B A A A B A A A B \n+A B B - A B B A A B B B B B B A A B A A A - A A B A B A B A B A B - B \n+B B A B A B A A - A B A B A B B A B A B B A A B A A A B A B B A B A A \n+A B A A B A \n+umc1038 A A A B B B A B B B B A B A A B A A A B A B A B \n+A B B B A A A A B A B B B - A A - A - B A B B A B B B A B A B A B - B \n+B B B B A B A B A A B A - A B B B B A B A A B B A A A B - B A B B B A \n+A B A A B - \n+-stop markers\n+-start traits\n+A_92_P022110\t1907.83\t1657.52\t1530.38\t2548.74\t1394.11\t2414.29\t1013.27\t1561.4\t1774.84\t1212.35\t2587.06\t2069.79\t1687.66\t1593.96\t2219.84\t1575.47\t879.98\t1049.07\t1146.33\t1266.84\t1383.36\t2099.17\t1207.23\t1123.14\t1225.54\t1760.81\t1738.8\t2366.49\t1107.37\t2256.14\t1105.67\t1667.55\t1409.59\t1654.87\t2633.21\t2066.46\t2310.44\t2318.99\t1750.23\t1492.78\t1934.55\t1748.27\t1539.58\t1290.06\t1196.4\t980.04\t2773.34\t1811.7\t1952.88\t2072.17\t2355.46\t1836.57\t1741.63\t1855.98\t1793.21\t1496.25\t1504.89\t1334.96\t2129.33\t1808.28\t1573.03\t1534.69\t2283.6\t1696.86\t874.28\t872.85\t761.49\t1199.3\t1203.38\t1573.04\t1258.05\t1649.04\t1178.29\t1427.65\t1595.21\t1677.65\t2118.77\t1632.53\t1966.77\t1609.6\t1738.82\t1623.54\t2245.36\t2401.11\t2002.04\t1376.94\t2626.52\t1626.31\t2032.78\t1566.47\t1873.58\t1791.24\t1935.08\t1847.94\t1657.56\t2080.53\t1876.91\t1709.47\t2577.11\t1681.43\n+A_92_P021792\t3383.7\t2858.51\t2452.5\t3265.75\t2169.88\t2843.6\t1710.32\t2513.63\t2350.09\t2482.3\t2811.97\t2395.43\t2817.64\t2832.13\t2268.09\t1578.41\t1625.86\t2212.96\t2168.45\t2133.59\t2660.8\t3544.02\t1919.65\t2792.2\t2432.98\t2470.68\t2831.19\t3301.27\t2100.74\t3346.37\t2209.62\t2224.38\t1734.25\t2214.3\t3030.25\t2771.25\t3023.16\t3493.25\t2527.49\t2147.3\t2720.76\t2796.01\t2976.3\t2084.86\t2233.18\t1905.63\t2789.6\t2311.73\t2481.62\t3157.47\t3071.01\t2289.1\t2358.61\t2987.19\t2494.79\t2794.48\t2638.42\t2183.94\t2721.58\t2057.09\t3640.91\t2383.45\t2817.01\t2488.33\t1212.52\t1407.59\t1026.75\t1924.1\t2490.45\t2530.32\t2098.66\t2317.95\t2050.7\t1947.59\t1984.52\t2326.34\t2917.57\t2139.23\t2405.29\t2146.24\t2706.49\t2419.42\t3075.2\t2615.3\t2934.66\t2139.47\t3150\t2442.85\t3681.64\t2282.22\t2875.73\t2772.08\t3358.95\t2402.17\t2077.22\t3048.38\t3636.61\t2211.56\t3208.42\t2550.24\n+A_92_P021634\t5007.91\t5395.51\t5003.4\t5920.93\t4347.67\t8893.35\t5730.41\t5404.74\t5427.28\t3862.22\t5747.74\t5517.62\t6150.08\t5568.19\t7561.59\t5515.57\t4661.37\t5397.6\t5762.04\t5718.6\t8143.61\t8408.78\t7023.18\t6318.82\t3830.66\t4544.4\t6847.62\t4360.47\t3511.04\t6550.79\t3088.44\t8117.16\t5485.32\t7506.46\t7622.19\t4327.43\t6379.47\t6204.9\t6154.42\t7899.39\t6757.04\t6449.08\t5826.2\t4744.89\t4058.95\t5860.34\t7286.87\t5140.84\t4774.45\t7484.8\t6227.06\t4556.72\t4812.59\t4625.75\t7193.47\t7112.51\t5438.96\t3334.73\t7295.72\t5102.24\t4875.7\t6941.31\t6125.25\t4558.38\t3420.65\t2031.74\t3182.04\t2511.67\t7339.69\t6154.25\t7747.87\t5576.7\t5599.8\t4716.2\t7019.85\t4835.27\t4222.55\t7610.92\t3906.32\t6923.87\t4877.57\t5414.54\t5207.33\t7880.67\t5926.36\t7441.39\t6312.49\t3859.27\t3056.63\t4680.94\t6149.93\t7344.85\t6666.22\t5394.55\t6472.55\t4955.89\t4852.57\t3776.41\t6988.17\t4900.4\n+-stop traits\n+-quit\n+-end\n' |
| b |
| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/input/qtlcart2.inp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/input/qtlcart2.inp Fri Mar 18 05:51:39 2016 -0400 |
| b |
| b'@@ -0,0 +1,692 @@\n+#bycross\n+-SampleSize 100\n+-Cross Ri1\n+-traits 4\n+-otraits 0\n+-missingtrait .\n+-case yes\n+-TranslationTable\n+AA\t2\tA\n+Aa\t1\t*1\n+aa\t0\tB\n+A-\t12\t*2\n+a-\t10\t*3\n+--\t-1\t-\n+-start markers\n+phi056 A A B B A B B A A A B A B A A A A A A A A A B A \n+B B A B - B B A B B - - A B A B A - - A B A A A A B A A A - B A B B - \n+A - B B B B A B A B A B - - A B A B A - B A A A A B A A B A B A A B A \n+B A B A A B \n+bnl5.62 A A - B A B B A B A B A B B A A A A A A A A B A \n+B A - B - A A A B A - A A B A B A B A A B A A A - B A A A B B A B B - \n+A A B B B B A B A B A A A - A B A B B A B A A - A B A A B A B B A B A \n+B A B A A B \n+umc1041 A A B B A A B A B B A B B A - A B A A A A B B A \n+A A B B - A A A B A B B B B B A - B A A B A A A - A A B - - B A B B B \n+A A B A B A A B A B A A A B A B A B A A B A - A A B A A B A B A A A A \n+B A B B A B \n+umc157a A A B A B A B A A B B - B A A A B - B A A A A A \n+A B B B - A A A B A A A B B A A B B B A A - B A A B A B A A B A A B B \n+A A B A B A A B B A A A A B A B B A B A A A A B A A B A B A B B A B A \n+B A B B B B \n+bnlg1178 A A A A B A B A A B B - B B A A B B B A A B A A \n+A B B B B A A A B A A A B B A A B B B A A - B A B - A B - A A - A B - \n+A A B A A A A B A A A A B B A - A A B B A A A B A A B - B - B B A B A \n+B A B B B B \n+bnlg1429 A A A A B A B A A B B B B B A A B - B A A B A A \n+A B B B B A A A B A A A B B A A B A B A A - B A B B A B - - A A B B - \n+B A B A A A A B A A A A A B A - A A B A A A A B A A B A B A A B A B A \n+B A B B B B \n+bnlg1627 A A A A B B A A B B A B B A A A B B B A A B A A \n+A B - B B A A A B A A A B B A A B A B A A - B A B B A B B - - A B B - \n+A A B A A A A B A B A A A B A B A A B A A A A B A A B A A A A B A B A \n+A A B B B B \n+umc11a A A - A B B B A B B A A B A A B B B B A A A - B \n+A B B B A B A A B B B A B B B A B A B A A B B A B - B B A B A B A B B \n+A A B B A A A B - B A A A B A B B A B A B - A B A A B B A B B - A B A \n+B A B B B B \n+bnlg439 A A A A B B A A B B A A - A A B B B B A A A B B \n+A B A B A A A A B B B A B B B B A A B A A B A B B - - B A B A B A B B \n+A B B A A A A B - B B A B B A - B B B B A A A B A - B A B B B - B - A \n+A A B B B B \n+bnlg2238 A A A - B B A A B B A B A A A B B A A A A A A B \n+A B A B A A A A B B B A A B B A A A - A A B A B B A A B A B A B - B B \n+A B B B A A A B B B B A A B A B B B B A A - A A A A A A A A A A B A A \n+A A - B B B \n+Bnlg1811_U A A A B B A A B B B B B A A A A B A A A A A A B \n+A B A B B B A A B B A A A B B A B A A A B B B B A A B B A B A B A B B \n+A B B B A A A B B B B A A B A B B B B A A A A B - B A B B B A A B A A \n+A A B B A B \n+bnlg2086 A B A A A A A A B B B B A A B - B A A B A A A B \n+A B A B B B A A B A B A A B B B B A A B B - A B B A B B A B B B A B B \n+B B B B A A A B B B A A A B B B - B B A - A A B B A A B B B A A B A A \n+A A A B A B \n+csu61b B B - A B A A A B B B B A B A - B B B B - B A B \n+B A A B B A A A B A B A A B B B B A - B A A - B - B B B A B B B A B B \n+A B B A A A A B B B A B A B A B - B B A - - A B A A - B B B A - B - A \n+A A B B A B \n+bnlg1057 B B A A A A B A B B B B A B A - B B A B B B B B \n+A B A B B A A A - A B A A B B B A A - A A A - B A - B B A - B B A B B \n+A B - A A A A - B A A B A B A B A B B A - B A B A A - B B B A - B - A \n+A A B B A B \n+umc1122 A B A A B A B A B B A B B B A A A B A B A B B A \n+B B A B B B A A B A B A A B B B A A B A A A B B A B B A A A B A A B A \n+A B A A A A B A B A B B A B A B A B B A A A B B A B B B B B B B B B B \n+A A B A A B \n+Bnlg615_U A A B A B B A A B A A B A B A B A B A A A B B B \n+B A A A B A A B B B B A A B B B A A B A A B B B A B B A A - B - A B A \n+A A B A B A B B B A B B A B - B A B B A A A B A A B B B A B B B B B B \n+A A B A A B \n+umc1128 A B B A B B B B B B B A A B A B A B A B A B B A \n+A A B A B A A B B B B A A B B B A A B A A B B B '..b'A A A A A A A A A B \n+B A A A B B B A A B A B B A B B A B A B A A A B A A A A B A A A A A B \n+A B A A A A A A B A B A A A B B A A A A A A A A A A A A A A A A A A A \n+B A B A A A \n+umc44a A B A B A B B A A B B B B B A A A A A A A A A B \n+B A B A B A B A A - B B A A B A A B A B A A A A - A - A B A B A A - B \n+A B A A A A A B B A A A A A A B A A A A A A A A A A A A A - B A A A A \n+B B B A A A \n+umc182 B B A B A B B A A B B B B B A A B A A B B A A B \n+A A B A B A B A B B B B B A B A A B A B A - A A B A B A B A B A A - B \n+A B B A A B A B B A A A A A A B A B A A A B A A A A A B A B B B A A A \n+B B B A B A \n+bnlg236 B A A B A B A A A B B A B B A A A A A B B A A B \n+A A B A B B B A B B B B B A B A A B A B A A A B B A B A B B B A A A B \n+A B B A A A A B B A A A A A A B A B A A A B A B A - A B A B B A A A A \n+A B B A B A \n+bnl7.49a B A - B B A A - A A A - A B A A A A A B B A A B \n+A - B A B B - A A B B B - B B A A A A A A - A B B A B A B B B A A - B \n+B A A A A B A A B A B A A A A B A B A A B - A - A B - B - B B - A A A \n+A B B A B A \n+bnlg1450 A A A B A B A A A B - A A B A B A A A B A A A B \n+A B B - A B B A A B B B B B B A A B A A A - A A B A B A B A B A B - B \n+B B A B A B A A - A B A B A B B A B A B B A A B A A A B A B B A B A A \n+A B A A B A \n+umc1038 A A A B B B A B B B B A B A A B A A A B A B A B \n+A B B B A A A A B A B B B - A A - A - B A B B A B B B A B A B A B - B \n+B B B B A B A B A A B A - A B B B B A B A A B B A A A B - B A B B B A \n+A B A A B - \n+-stop markers\n+-start traits\n+A_92_P037834\t614.76\t480\t159.36\t366.3\t294.97\t122.92\t322.5\t168.7\t350.87\t555.45\t228.25\t924.42\t.\t.\t733.53\t1406.06\t471.19\t291.21\t599.91\t1184.39\t1811.05\t481.8\t2288.62\t771.68\t.\t.\t776.6\t267.51\t936.66\t335.22\t.\t.\t.\t.\t407.66\t552.37\t363.69\t640.53\t605.49\t212.99\t322.26\t233.7\t359.58\t180.01\t1448.65\t1968.31\t348.1\t1787.13\t.\t.\t252.92\t286.18\t365.86\t299.67\t439.85\t195.04\t251.41\t155.69\t447.4\t922.52\t616.42\t278.46\t469.08\t406.14\t.\t.\t.\t.\t.\t.\t1544.27\t829.77\t789.32\t314.05\t1940.39\t573.41\t1188.84\t1069.96\t416.56\t850.32\t1126.01\t136.73\t684.91\t262.46\t1301.09\t404.64\t.\t.\t517.48\t314.27\t439.91\t312.15\t432.45\t857.77\t599.45\t406.9\t.\t.\t563.83\t1052.15\n+A_92_P037509\t.\t.\t.\t.\t157.2\t339.31\t177.76\t216.87\t167.97\t389.94\t.\t.\t361.74\t440.07\t.\t.\t.\t.\t141.59\t193.48\t.\t.\t298.22\t98.91\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t474.05\t104.32\t.\t.\t265.64\t344.79\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t184.48\t225.23\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t81.82\t324.04\t159.19\t128.64\t326.25\t94.29\t250.2\t86.44\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t303.92\t167.72\t.\t.\t.\t.\t390.07\t124.47\t.\t.\t.\t.\n+A_92_P037035\t1385.12\t791.49\t375.74\t972.44\t566.72\t1136.6\t692.64\t395.81\t537.73\t821.82\t643.84\t566.22\t1071.02\t541.94\t1680.95\t2004.63\t383.42\t779.75\t496.22\t1138.04\t993.13\t586.42\t925.9\t467.27\t419.34\t767.3\t1325.63\t927.63\t2382.87\t1398.41\t731.01\t693.42\t577.22\t1434.44\t1709.52\t584.7\t601.51\t1118.4\t1566.44\t283.84\t165.7\t612.32\t1359.47\t319.07\t1163.17\t4658.47\t1019.44\t813.34\t887.19\t1743.35\t1648.64\t533.28\t699.33\t447.82\t931.22\t517.95\t665.55\t341.87\t754.27\t1386.56\t1235.85\t583.05\t1174.4\t531.88\t.\t.\t.\t.\t1029.62\t612.14\t1463.99\t701.39\t819.65\t520.84\t1452.92\t1772.76\t3964.91\t817.77\t392.82\t1805.64\t1920.01\t384.42\t1381.15\t1157.34\t3067.84\t1553.18\t537.23\t565.3\t1209.88\t830.18\t1898.84\t557.04\t2182.55\t1310.4\t548.53\t722.11\t675.48\t468.94\t720.57\t1335.18\n+A_92_P036877\t799.28\t939.06\t727.02\t1209.68\t1847.99\t775.6\t288.31\t270.58\t494.41\t889.64\t873.03\t1321.07\t1111.45\t1022.83\t1545.7\t2083.47\t746.07\t349.71\t508.35\t1253.53\t1584.3\t654.29\t1093.3\t638.98\t778.89\t883.46\t752.2\t767.14\t1779.18\t427.23\t.\t.\t.\t.\t443.49\t1768.67\t833.91\t437.6\t719.94\t715.83\t574.77\t783.37\t441.88\t305.04\t1269.3\t2758.96\t971.84\t1272.12\t634.76\t358.35\t733.71\t770.66\t508.1\t631.74\t772.54\t328.11\t679.57\t320.39\t472.06\t2269\t602.58\t441.86\t1017.69\t926.28\t.\t.\t.\t.\t796.43\t1127.55\t1314.04\t858.73\t1064.51\t360.01\t941.3\t772.42\t1022.28\t1185.29\t911.06\t759.69\t931.43\t672.8\t917.17\t1451.34\t724.72\t946.06\t1320.09\t782.91\t903.17\t755.9\t516.06\t396.13\t457.3\t1015.71\t465.17\t1144.43\t281.76\t546.66\t1273.41\t908.38\n+-stop traits\n+-quit\n+-end\n' |
| b |
| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/input/qtlcart3.inp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/input/qtlcart3.inp Fri Mar 18 05:51:39 2016 -0400 |
| b |
| b'@@ -0,0 +1,692 @@\n+#bycross\n+-SampleSize 100\n+-Cross Ri1\n+-traits 4\n+-otraits 0\n+-missingtrait .\n+-case yes\n+-TranslationTable\n+AA\t2\tA\n+Aa\t1\t*1\n+aa\t0\tB\n+A-\t12\t*2\n+a-\t10\t*3\n+--\t-1\t-\n+-start markers\n+phi056 A A B B A B B A A A B A B A A A A A A A A A B A \n+B B A B - B B A B B - - A B A B A - - A B A A A A B A A A - B A B B - \n+A - B B B B A B A B A B - - A B A B A - B A A A A B A A B A B A A B A \n+B A B A A B \n+bnl5.62 A A - B A B B A B A B A B B A A A A A A A A B A \n+B A - B - A A A B A - A A B A B A B A A B A A A - B A A A B B A B B - \n+A A B B B B A B A B A A A - A B A B B A B A A - A B A A B A B B A B A \n+B A B A A B \n+umc1041 A A B B A A B A B B A B B A - A B A A A A B B A \n+A A B B - A A A B A B B B B B A - B A A B A A A - A A B - - B A B B B \n+A A B A B A A B A B A A A B A B A B A A B A - A A B A A B A B A A A A \n+B A B B A B \n+umc157a A A B A B A B A A B B - B A A A B - B A A A A A \n+A B B B - A A A B A A A B B A A B B B A A - B A A B A B A A B A A B B \n+A A B A B A A B B A A A A B A B B A B A A A A B A A B A B A B B A B A \n+B A B B B B \n+bnlg1178 A A A A B A B A A B B - B B A A B B B A A B A A \n+A B B B B A A A B A A A B B A A B B B A A - B A B - A B - A A - A B - \n+A A B A A A A B A A A A B B A - A A B B A A A B A A B - B - B B A B A \n+B A B B B B \n+bnlg1429 A A A A B A B A A B B B B B A A B - B A A B A A \n+A B B B B A A A B A A A B B A A B A B A A - B A B B A B - - A A B B - \n+B A B A A A A B A A A A A B A - A A B A A A A B A A B A B A A B A B A \n+B A B B B B \n+bnlg1627 A A A A B B A A B B A B B A A A B B B A A B A A \n+A B - B B A A A B A A A B B A A B A B A A - B A B B A B B - - A B B - \n+A A B A A A A B A B A A A B A B A A B A A A A B A A B A A A A B A B A \n+A A B B B B \n+umc11a A A - A B B B A B B A A B A A B B B B A A A - B \n+A B B B A B A A B B B A B B B A B A B A A B B A B - B B A B A B A B B \n+A A B B A A A B - B A A A B A B B A B A B - A B A A B B A B B - A B A \n+B A B B B B \n+bnlg439 A A A A B B A A B B A A - A A B B B B A A A B B \n+A B A B A A A A B B B A B B B B A A B A A B A B B - - B A B A B A B B \n+A B B A A A A B - B B A B B A - B B B B A A A B A - B A B B B - B - A \n+A A B B B B \n+bnlg2238 A A A - B B A A B B A B A A A B B A A A A A A B \n+A B A B A A A A B B B A A B B A A A - A A B A B B A A B A B A B - B B \n+A B B B A A A B B B B A A B A B B B B A A - A A A A A A A A A A B A A \n+A A - B B B \n+Bnlg1811_U A A A B B A A B B B B B A A A A B A A A A A A B \n+A B A B B B A A B B A A A B B A B A A A B B B B A A B B A B A B A B B \n+A B B B A A A B B B B A A B A B B B B A A A A B - B A B B B A A B A A \n+A A B B A B \n+bnlg2086 A B A A A A A A B B B B A A B - B A A B A A A B \n+A B A B B B A A B A B A A B B B B A A B B - A B B A B B A B B B A B B \n+B B B B A A A B B B A A A B B B - B B A - A A B B A A B B B A A B A A \n+A A A B A B \n+csu61b B B - A B A A A B B B B A B A - B B B B - B A B \n+B A A B B A A A B A B A A B B B B A - B A A - B - B B B A B B B A B B \n+A B B A A A A B B B A B A B A B - B B A - - A B A A - B B B A - B - A \n+A A B B A B \n+bnlg1057 B B A A A A B A B B B B A B A - B B A B B B B B \n+A B A B B A A A - A B A A B B B A A - A A A - B A - B B A - B B A B B \n+A B - A A A A - B A A B A B A B A B B A - B A B A A - B B B A - B - A \n+A A B B A B \n+umc1122 A B A A B A B A B B A B B B A A A B A B A B B A \n+B B A B B B A A B A B A A B B B A A B A A A B B A B B A A A B A A B A \n+A B A A A A B A B A B B A B A B A B B A A A B B A B B B B B B B B B B \n+A A B A A B \n+Bnlg615_U A A B A B B A A B A A B A B A B A B A A A B B B \n+B A A A B A A B B B B A A B B B A A B A A B B B A B B A A - B - A B A \n+A A B A B A B B B A B B A B - B A B B A A A B A A B B B A B B B B B B \n+A A B A A B \n+umc1128 A B B A B B B B B B B A A B A B A B A B A B B A \n+A A B A B A A B B B B A A B B B A A B A A B B B '..b' A B A A A A A A \n+B B B A A A \n+npi232a A B A B A B B A A B B B A B A A A A A A A A A B \n+B A A A B B B A A B A B B A B B A B A B A A A B A A A A B A A A A A B \n+A B A A A A A A B A B A A A B B A A A A A A A A A A A A A A A A A A A \n+B A B A A A \n+umc44a A B A B A B B A A B B B B B A A A A A A A A A B \n+B A B A B A B A A - B B A A B A A B A B A A A A - A - A B A B A A - B \n+A B A A A A A B B A A A A A A B A A A A A A A A A A A A A - B A A A A \n+B B B A A A \n+umc182 B B A B A B B A A B B B B B A A B A A B B A A B \n+A A B A B A B A B B B B B A B A A B A B A - A A B A B A B A B A A - B \n+A B B A A B A B B A A A A A A B A B A A A B A A A A A B A B B B A A A \n+B B B A B A \n+bnlg236 B A A B A B A A A B B A B B A A A A A B B A A B \n+A A B A B B B A B B B B B A B A A B A B A A A B B A B A B B B A A A B \n+A B B A A A A B B A A A A A A B A B A A A B A B A - A B A B B A A A A \n+A B B A B A \n+bnl7.49a B A - B B A A - A A A - A B A A A A A B B A A B \n+A - B A B B - A A B B B - B B A A A A A A - A B B A B A B B B A A - B \n+B A A A A B A A B A B A A A A B A B A A B - A - A B - B - B B - A A A \n+A B B A B A \n+bnlg1450 A A A B A B A A A B - A A B A B A A A B A A A B \n+A B B - A B B A A B B B B B B A A B A A A - A A B A B A B A B A B - B \n+B B A B A B A A - A B A B A B B A B A B B A A B A A A B A B B A B A A \n+A B A A B A \n+umc1038 A A A B B B A B B B B A B A A B A A A B A B A B \n+A B B B A A A A B A B B B - A A - A - B A B B A B B B A B A B A B - B \n+B B B B A B A B A A B A - A B B B B A B A A B B A A A B - B A B B B A \n+A B A A B - \n+-stop markers\n+-start traits\n+A_92_P036723\t.\t.\t.\t.\t.\t.\t214.95\t159.26\t130.76\t178.45\t265.89\t220.27\t.\t.\t.\t.\t282.1\t219.72\t204.9\t179.84\t254.69\t300.6\t173.81\t191.32\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t155.74\t260.45\t251.73\t230.09\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t214.72\t262.26\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t281.56\t124.42\t.\t.\t.\t.\t204.43\t185.07\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t233.71\t292.11\t.\t.\t129.64\t156.01\t217.89\t199.59\t.\t.\t.\t.\n+A_92_P036564\t688.45\t1036.72\t829.29\t1023.7\t1124.77\t1129.93\t1344.41\t1376.92\t706.75\t1064.56\t805.5\t1325.39\t1422.2\t2347.35\t1116.96\t544.53\t1523.09\t1358.2\t1527.44\t1409.87\t1883.67\t1993.77\t1470.3\t2089.67\t2467.94\t1244.11\t619.43\t718.9\t865.05\t2068.72\t1815.05\t775.96\t1264.67\t881.18\t659.17\t1082.76\t973.36\t344.52\t566.44\t813.6\t2261.25\t1590.47\t294.79\t1053.43\t2433.67\t1442.05\t1269.95\t1440.85\t.\t.\t872.73\t1821.32\t925.74\t1584.09\t1137.02\t1065.68\t1498.58\t625.33\t1371.9\t736.02\t1291.02\t1442.08\t1470.73\t730.02\t243.99\t430.01\t.\t.\t1454.86\t943.96\t1207.53\t1469.43\t788.14\t921.6\t470.98\t1923.57\t301.86\t1406.16\t1101.23\t835.82\t476.27\t1584.52\t683.88\t1746.45\t541.21\t718.65\t1902.22\t1810.05\t935.15\t856\t589.43\t1476.37\t614.15\t1182.36\t886.17\t1212.48\t659.08\t1212.01\t1377.43\t1264.51\n+A_92_P036402\t.\t.\t.\t.\t205.78\t116.83\t245.79\t129.1\t158.94\t244.84\t175.33\t237.51\t239.5\t256.92\t.\t.\t290.74\t194.45\t.\t.\t519.62\t189.22\t207.99\t226.4\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t192.59\t281.57\t.\t.\t.\t.\t.\t.\t231.54\t276.58\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t132.24\t236.38\t.\t.\t.\t.\t.\t.\t.\t.\t164.17\t104.86\t285.28\t230.22\t220.39\t191.88\t187.62\t276.29\t272.61\t217.36\t.\t.\t.\t.\t.\t.\t.\t.\t226.03\t328.24\t126.41\t186.82\t131.66\t286.51\t212.36\t173.64\t.\t.\t.\t.\n+A_92_P036241\t841.85\t2197.26\t2085.55\t1763.91\t2332.38\t2291.68\t1643.32\t1567.36\t2470.48\t2161.4\t2445.94\t2515.19\t2733.92\t2122.02\t2787.49\t4813.41\t1586.2\t1618.55\t1322.94\t2099.28\t2883.46\t2490.3\t1917.43\t2032.65\t2201.64\t2263.6\t1850.72\t1110.89\t2683.28\t1840.16\t1516.63\t2834.64\t2844.76\t2313.01\t2454.84\t2552.41\t2559.55\t1081.76\t2493.14\t2069.69\t1784.29\t1532.65\t642.74\t1132.19\t3563.78\t3149.46\t2412.15\t2508.47\t1849.12\t1565.43\t1652.9\t1876.16\t2263.8\t1879.86\t2475.94\t2020.11\t2356.92\t2211.49\t2102.42\t3070.38\t2207.57\t2421.25\t2238.1\t2446.2\t567.97\t512.97\t.\t.\t1773.26\t1306.58\t2085.71\t1684.65\t2159.45\t1792.38\t3104.79\t2830.93\t1209.97\t2582.06\t2462.47\t2942.99\t1360.03\t1819.24\t1325.41\t2527.83\t1531.68\t3216.05\t2065.34\t2042.42\t1334.74\t2473.6\t1584.24\t2105.07\t1698.06\t2584.35\t1919.43\t2187.06\t1601.91\t1430.88\t2272.29\t2858.92\n+-stop traits\n+-quit\n+-end\n' |
| b |
| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/input/qtlcart4.inp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/input/qtlcart4.inp Fri Mar 18 05:51:39 2016 -0400 |
| b |
| b'@@ -0,0 +1,692 @@\n+#bycross\n+-SampleSize 100\n+-Cross Ri1\n+-traits 4\n+-otraits 0\n+-missingtrait .\n+-case yes\n+-TranslationTable\n+AA\t2\tA\n+Aa\t1\t*1\n+aa\t0\tB\n+A-\t12\t*2\n+a-\t10\t*3\n+--\t-1\t-\n+-start markers\n+phi056 A A B B A B B A A A B A B A A A A A A A A A B A \n+B B A B - B B A B B - - A B A B A - - A B A A A A B A A A - B A B B - \n+A - B B B B A B A B A B - - A B A B A - B A A A A B A A B A B A A B A \n+B A B A A B \n+bnl5.62 A A - B A B B A B A B A B B A A A A A A A A B A \n+B A - B - A A A B A - A A B A B A B A A B A A A - B A A A B B A B B - \n+A A B B B B A B A B A A A - A B A B B A B A A - A B A A B A B B A B A \n+B A B A A B \n+umc1041 A A B B A A B A B B A B B A - A B A A A A B B A \n+A A B B - A A A B A B B B B B A - B A A B A A A - A A B - - B A B B B \n+A A B A B A A B A B A A A B A B A B A A B A - A A B A A B A B A A A A \n+B A B B A B \n+umc157a A A B A B A B A A B B - B A A A B - B A A A A A \n+A B B B - A A A B A A A B B A A B B B A A - B A A B A B A A B A A B B \n+A A B A B A A B B A A A A B A B B A B A A A A B A A B A B A B B A B A \n+B A B B B B \n+bnlg1178 A A A A B A B A A B B - B B A A B B B A A B A A \n+A B B B B A A A B A A A B B A A B B B A A - B A B - A B - A A - A B - \n+A A B A A A A B A A A A B B A - A A B B A A A B A A B - B - B B A B A \n+B A B B B B \n+bnlg1429 A A A A B A B A A B B B B B A A B - B A A B A A \n+A B B B B A A A B A A A B B A A B A B A A - B A B B A B - - A A B B - \n+B A B A A A A B A A A A A B A - A A B A A A A B A A B A B A A B A B A \n+B A B B B B \n+bnlg1627 A A A A B B A A B B A B B A A A B B B A A B A A \n+A B - B B A A A B A A A B B A A B A B A A - B A B B A B B - - A B B - \n+A A B A A A A B A B A A A B A B A A B A A A A B A A B A A A A B A B A \n+A A B B B B \n+umc11a A A - A B B B A B B A A B A A B B B B A A A - B \n+A B B B A B A A B B B A B B B A B A B A A B B A B - B B A B A B A B B \n+A A B B A A A B - B A A A B A B B A B A B - A B A A B B A B B - A B A \n+B A B B B B \n+bnlg439 A A A A B B A A B B A A - A A B B B B A A A B B \n+A B A B A A A A B B B A B B B B A A B A A B A B B - - B A B A B A B B \n+A B B A A A A B - B B A B B A - B B B B A A A B A - B A B B B - B - A \n+A A B B B B \n+bnlg2238 A A A - B B A A B B A B A A A B B A A A A A A B \n+A B A B A A A A B B B A A B B A A A - A A B A B B A A B A B A B - B B \n+A B B B A A A B B B B A A B A B B B B A A - A A A A A A A A A A B A A \n+A A - B B B \n+Bnlg1811_U A A A B B A A B B B B B A A A A B A A A A A A B \n+A B A B B B A A B B A A A B B A B A A A B B B B A A B B A B A B A B B \n+A B B B A A A B B B B A A B A B B B B A A A A B - B A B B B A A B A A \n+A A B B A B \n+bnlg2086 A B A A A A A A B B B B A A B - B A A B A A A B \n+A B A B B B A A B A B A A B B B B A A B B - A B B A B B A B B B A B B \n+B B B B A A A B B B A A A B B B - B B A - A A B B A A B B B A A B A A \n+A A A B A B \n+csu61b B B - A B A A A B B B B A B A - B B B B - B A B \n+B A A B B A A A B A B A A B B B B A - B A A - B - B B B A B B B A B B \n+A B B A A A A B B B A B A B A B - B B A - - A B A A - B B B A - B - A \n+A A B B A B \n+bnlg1057 B B A A A A B A B B B B A B A - B B A B B B B B \n+A B A B B A A A - A B A A B B B A A - A A A - B A - B B A - B B A B B \n+A B - A A A A - B A A B A B A B A B B A - B A B A A - B B B A - B - A \n+A A B B A B \n+umc1122 A B A A B A B A B B A B B B A A A B A B A B B A \n+B B A B B B A A B A B A A B B B A A B A A A B B A B B A A A B A A B A \n+A B A A A A B A B A B B A B A B A B B A A A B B A B B B B B B B B B B \n+A A B A A B \n+Bnlg615_U A A B A B B A A B A A B A B A B A B A A A B B B \n+B A A A B A A B B B B A A B B B A A B A A B B B A B B A A - B - A B A \n+A A B A B A B B B A B B A B - B A B B A A A B A A B B B A B B B B B B \n+A A B A A B \n+umc1128 A B B A B B B B B B B A A B A B A B A B A B B A \n+A A B A B A A B B B B A A B B B A A B A A B B B '..b'B A B B A B B A B A B A A A B A A A A B A A A A A B \n+A B A A A A A A B A B A A A B B A A A A A A A A A A A A A A A A A A A \n+B A B A A A \n+umc44a A B A B A B B A A B B B B B A A A A A A A A A B \n+B A B A B A B A A - B B A A B A A B A B A A A A - A - A B A B A A - B \n+A B A A A A A B B A A A A A A B A A A A A A A A A A A A A - B A A A A \n+B B B A A A \n+umc182 B B A B A B B A A B B B B B A A B A A B B A A B \n+A A B A B A B A B B B B B A B A A B A B A - A A B A B A B A B A A - B \n+A B B A A B A B B A A A A A A B A B A A A B A A A A A B A B B B A A A \n+B B B A B A \n+bnlg236 B A A B A B A A A B B A B B A A A A A B B A A B \n+A A B A B B B A B B B B B A B A A B A B A A A B B A B A B B B A A A B \n+A B B A A A A B B A A A A A A B A B A A A B A B A - A B A B B A A A A \n+A B B A B A \n+bnl7.49a B A - B B A A - A A A - A B A A A A A B B A A B \n+A - B A B B - A A B B B - B B A A A A A A - A B B A B A B B B A A - B \n+B A A A A B A A B A B A A A A B A B A A B - A - A B - B - B B - A A A \n+A B B A B A \n+bnlg1450 A A A B A B A A A B - A A B A B A A A B A A A B \n+A B B - A B B A A B B B B B B A A B A A A - A A B A B A B A B A B - B \n+B B A B A B A A - A B A B A B B A B A B B A A B A A A B A B B A B A A \n+A B A A B A \n+umc1038 A A A B B B A B B B B A B A A B A A A B A B A B \n+A B B B A A A A B A B B B - A A - A - B A B B A B B B A B A B A B - B \n+B B B B A B A B A A B A - A B B B B A B A A B B A A A B - B A B B B A \n+A B A A B - \n+-stop markers\n+-start traits\n+A_92_P036076\t337.24\t192.57\t145.39\t1402.89\t.\t.\t964.96\t1708.51\t304.95\t1101.35\t320.38\t193.12\t1451.14\t167.94\t.\t.\t96.3\t800.87\t139.18\t136.44\t183.73\t2461.54\t1073.34\t178.39\t1461.14\t1085.66\t983.5\t342.4\t.\t.\t.\t.\t.\t.\t1212.94\t139.79\t1725.86\t347.78\t200.02\t1789.14\t1055.94\t1088.89\t.\t.\t.\t.\t274.79\t211.29\t.\t.\t1228.12\t238.49\t.\t.\t1175.17\t1067.33\t948.86\t147.82\t.\t.\t1966.57\t147.95\t.\t.\t.\t.\t.\t.\t.\t.\t167.19\t215.65\t844.02\t153.81\t1247.11\t154.19\t263.84\t1076.07\t1221.1\t155.34\t234.24\t234.2\t.\t.\t.\t.\t.\t.\t1419.55\t875.02\t243.07\t1164.98\t357.29\t184.37\t1105.99\t1185.83\t1397.61\t1008.11\t1261.97\t947.65\n+A_92_P035602\t276.08\t399.48\t427.32\t431.95\t481.33\t551.25\t330.95\t433.98\t207.05\t484.45\t454.93\t355.93\t502.47\t230.41\t370.61\t223.59\t359.18\t491.33\t450.79\t298.18\t475.73\t828.33\t343.42\t440.98\t408.26\t456.47\t.\t.\t434.11\t429.5\t.\t.\t.\t.\t250.09\t539.26\t767.69\t216.45\t508.12\t211.16\t250.49\t448.41\t221.92\t273.95\t535.28\t748.74\t840.81\t596\t413.63\t358.58\t238.65\t317.79\t445.08\t335.93\t278.49\t228.52\t221.47\t537.13\t448.46\t397.44\t194.18\t507.01\t582\t375.24\t.\t.\t.\t.\t296.56\t326.66\t470.05\t461.32\t213.76\t257.86\t407.43\t220.57\t474.38\t212.31\t.\t.\t289.05\t409.87\t381.11\t613.75\t254.07\t408.43\t.\t.\t304.34\t512.02\t443.96\t419.09\t506.78\t393.27\t523.28\t499.06\t492.48\t215.27\t172.49\t560.17\n+A_92_P035118\t.\t.\t287.6\t331.99\t.\t.\t.\t.\t326.72\t180.28\t263.54\t318.41\t345.53\t355.88\t317.32\t514.08\t310.68\t192.73\t414.15\t509.07\t509.63\t280.86\t539.73\t217.23\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t294.62\t185.25\t256.06\t447.73\t286.17\t251.12\t158.54\t190.12\t194.96\t106.49\t584.87\t748.51\t722.04\t637.92\t.\t.\t247.25\t291.1\t.\t.\t.\t.\t283.81\t227.91\t.\t.\t232.89\t341.3\t.\t.\t.\t.\t.\t.\t208.7\t428.69\t462.59\t253.69\t.\t.\t249.27\t471.95\t376.23\t196.86\t196.2\t515.09\t370.87\t252.5\t228.52\t168.9\t682.57\t302.11\t253.67\t283.18\t371.2\t360.78\t269.88\t274.96\t260.94\t534.33\t250.4\t204.31\t.\t.\t212.19\t434.94\n+A_92_P034955\t855.74\t780.62\t904.92\t896.73\t755.68\t577.51\t861.74\t795.06\t802.74\t1011.2\t764.62\t719.35\t852.4\t831.01\t.\t.\t2061.52\t1554.96\t1461.83\t1636.98\t3265.39\t1909.64\t1913.44\t1522.54\t677.43\t800.93\t567.19\t891.91\t521.28\t649.47\t992.21\t881.95\t.\t.\t491.71\t756.91\t652.6\t877.23\t1048.87\t809.13\t906.27\t990.88\t539.09\t841.48\t1767.71\t2031.15\t690.51\t975.18\t467.13\t505.51\t465.47\t714.89\t540.58\t656.98\t717.77\t738.66\t528.63\t534.43\t653.26\t661.8\t597.78\t760.44\t550.59\t840.06\t.\t.\t.\t.\t1460.68\t1550.99\t1340.65\t1474.77\t676.07\t662.09\t767.4\t747.21\t636.01\t1079.85\t1060.81\t755.07\t488.41\t484.53\t573.07\t753.02\t628.96\t781.58\t547.29\t670.84\t503.26\t659.41\t849.42\t896.81\t742.25\t943.1\t815.67\t736.61\t457.19\t467.19\t720.08\t655.16\n+-stop traits\n+-quit\n+-end\n' |
| b |
| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/input/qtlcart5.inp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/input/qtlcart5.inp Fri Mar 18 05:51:39 2016 -0400 |
| b |
| b'@@ -0,0 +1,692 @@\n+#bycross\n+-SampleSize 100\n+-Cross Ri1\n+-traits 4\n+-otraits 0\n+-missingtrait .\n+-case yes\n+-TranslationTable\n+AA\t2\tA\n+Aa\t1\t*1\n+aa\t0\tB\n+A-\t12\t*2\n+a-\t10\t*3\n+--\t-1\t-\n+-start markers\n+phi056 A A B B A B B A A A B A B A A A A A A A A A B A \n+B B A B - B B A B B - - A B A B A - - A B A A A A B A A A - B A B B - \n+A - B B B B A B A B A B - - A B A B A - B A A A A B A A B A B A A B A \n+B A B A A B \n+bnl5.62 A A - B A B B A B A B A B B A A A A A A A A B A \n+B A - B - A A A B A - A A B A B A B A A B A A A - B A A A B B A B B - \n+A A B B B B A B A B A A A - A B A B B A B A A - A B A A B A B B A B A \n+B A B A A B \n+umc1041 A A B B A A B A B B A B B A - A B A A A A B B A \n+A A B B - A A A B A B B B B B A - B A A B A A A - A A B - - B A B B B \n+A A B A B A A B A B A A A B A B A B A A B A - A A B A A B A B A A A A \n+B A B B A B \n+umc157a A A B A B A B A A B B - B A A A B - B A A A A A \n+A B B B - A A A B A A A B B A A B B B A A - B A A B A B A A B A A B B \n+A A B A B A A B B A A A A B A B B A B A A A A B A A B A B A B B A B A \n+B A B B B B \n+bnlg1178 A A A A B A B A A B B - B B A A B B B A A B A A \n+A B B B B A A A B A A A B B A A B B B A A - B A B - A B - A A - A B - \n+A A B A A A A B A A A A B B A - A A B B A A A B A A B - B - B B A B A \n+B A B B B B \n+bnlg1429 A A A A B A B A A B B B B B A A B - B A A B A A \n+A B B B B A A A B A A A B B A A B A B A A - B A B B A B - - A A B B - \n+B A B A A A A B A A A A A B A - A A B A A A A B A A B A B A A B A B A \n+B A B B B B \n+bnlg1627 A A A A B B A A B B A B B A A A B B B A A B A A \n+A B - B B A A A B A A A B B A A B A B A A - B A B B A B B - - A B B - \n+A A B A A A A B A B A A A B A B A A B A A A A B A A B A A A A B A B A \n+A A B B B B \n+umc11a A A - A B B B A B B A A B A A B B B B A A A - B \n+A B B B A B A A B B B A B B B A B A B A A B B A B - B B A B A B A B B \n+A A B B A A A B - B A A A B A B B A B A B - A B A A B B A B B - A B A \n+B A B B B B \n+bnlg439 A A A A B B A A B B A A - A A B B B B A A A B B \n+A B A B A A A A B B B A B B B B A A B A A B A B B - - B A B A B A B B \n+A B B A A A A B - B B A B B A - B B B B A A A B A - B A B B B - B - A \n+A A B B B B \n+bnlg2238 A A A - B B A A B B A B A A A B B A A A A A A B \n+A B A B A A A A B B B A A B B A A A - A A B A B B A A B A B A B - B B \n+A B B B A A A B B B B A A B A B B B B A A - A A A A A A A A A A B A A \n+A A - B B B \n+Bnlg1811_U A A A B B A A B B B B B A A A A B A A A A A A B \n+A B A B B B A A B B A A A B B A B A A A B B B B A A B B A B A B A B B \n+A B B B A A A B B B B A A B A B B B B A A A A B - B A B B B A A B A A \n+A A B B A B \n+bnlg2086 A B A A A A A A B B B B A A B - B A A B A A A B \n+A B A B B B A A B A B A A B B B B A A B B - A B B A B B A B B B A B B \n+B B B B A A A B B B A A A B B B - B B A - A A B B A A B B B A A B A A \n+A A A B A B \n+csu61b B B - A B A A A B B B B A B A - B B B B - B A B \n+B A A B B A A A B A B A A B B B B A - B A A - B - B B B A B B B A B B \n+A B B A A A A B B B A B A B A B - B B A - - A B A A - B B B A - B - A \n+A A B B A B \n+bnlg1057 B B A A A A B A B B B B A B A - B B A B B B B B \n+A B A B B A A A - A B A A B B B A A - A A A - B A - B B A - B B A B B \n+A B - A A A A - B A A B A B A B A B B A - B A B A A - B B B A - B - A \n+A A B B A B \n+umc1122 A B A A B A B A B B A B B B A A A B A B A B B A \n+B B A B B B A A B A B A A B B B A A B A A A B B A B B A A A B A A B A \n+A B A A A A B A B A B B A B A B A B B A A A B B A B B B B B B B B B B \n+A A B A A B \n+Bnlg615_U A A B A B B A A B A A B A B A B A B A A A B B B \n+B A A A B A A B B B B A A B B B A A B A A B B B A B B A A - B - A B A \n+A A B A B A B B B A B B A B - B A B B A A A B A A B B B A B B B B B B \n+A A B A A B \n+umc1128 A B B A B B B B B B B A A B A B A B A B A B B A \n+A A B A B A A B B B B A A B B B A A B A A B B B '..b'A A A A A B \n+A B A A B A A A B A B A A A B B A A B A B A A A A A A A B A A A A A A \n+B B B A A A \n+npi232a A B A B A B B A A B B B A B A A A A A A A A A B \n+B A A A B B B A A B A B B A B B A B A B A A A B A A A A B A A A A A B \n+A B A A A A A A B A B A A A B B A A A A A A A A A A A A A A A A A A A \n+B A B A A A \n+umc44a A B A B A B B A A B B B B B A A A A A A A A A B \n+B A B A B A B A A - B B A A B A A B A B A A A A - A - A B A B A A - B \n+A B A A A A A B B A A A A A A B A A A A A A A A A A A A A - B A A A A \n+B B B A A A \n+umc182 B B A B A B B A A B B B B B A A B A A B B A A B \n+A A B A B A B A B B B B B A B A A B A B A - A A B A B A B A B A A - B \n+A B B A A B A B B A A A A A A B A B A A A B A A A A A B A B B B A A A \n+B B B A B A \n+bnlg236 B A A B A B A A A B B A B B A A A A A B B A A B \n+A A B A B B B A B B B B B A B A A B A B A A A B B A B A B B B A A A B \n+A B B A A A A B B A A A A A A B A B A A A B A B A - A B A B B A A A A \n+A B B A B A \n+bnl7.49a B A - B B A A - A A A - A B A A A A A B B A A B \n+A - B A B B - A A B B B - B B A A A A A A - A B B A B A B B B A A - B \n+B A A A A B A A B A B A A A A B A B A A B - A - A B - B - B B - A A A \n+A B B A B A \n+bnlg1450 A A A B A B A A A B - A A B A B A A A B A A A B \n+A B B - A B B A A B B B B B B A A B A A A - A A B A B A B A B A B - B \n+B B A B A B A A - A B A B A B B A B A B B A A B A A A B A B B A B A A \n+A B A A B A \n+umc1038 A A A B B B A B B B B A B A A B A A A B A B A B \n+A B B B A A A A B A B B B - A A - A - B A B B A B B B A B A B A B - B \n+B B B B A B A B A A B A - A B B B B A B A A B B A A A B - B A B B B A \n+A B A A B - \n+-stop markers\n+-start traits\n+A_92_P034794\t272.3\t355.1\t343.78\t429.3\t245.13\t214.2\t240.07\t196.07\t277.78\t286.51\t352.24\t226.24\t376.78\t361.17\t.\t.\t209.52\t156.03\t275.69\t238.66\t315.01\t193.89\t222.99\t173.06\t.\t.\t280.04\t344.1\t367.27\t392.39\t.\t.\t.\t.\t198.26\t239.79\t295.38\t309.99\t283.58\t193.49\t342.71\t156.23\t126.42\t176.16\t406.6\t340.19\t296.8\t267.07\t.\t.\t426.45\t355.73\t457.91\t181.2\t399.16\t263.35\t164.93\t198.17\t275.66\t338.5\t.\t.\t300.51\t456.49\t529.29\t391.64\t.\t.\t242.23\t166.51\t259.62\t246.07\t245.25\t247.9\t.\t.\t201.39\t372.05\t356.35\t198.44\t361.37\t205.86\t432.95\t427.4\t347.36\t196.78\t368.06\t308\t609.54\t474.31\t216.44\t284.08\t278.13\t478.09\t455.59\t384.76\t299.25\t238.53\t351.81\t344.56\n+A_92_P034308\t188.32\t231.11\t.\t.\t287.39\t127.43\t.\t.\t184.48\t217.8\t95.91\t303.01\t256.13\t171.32\t.\t.\t187.66\t141.42\t165.74\t237.05\t.\t.\t169.38\t214.18\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t112.78\t187.69\t290.05\t229.06\t.\t.\t.\t.\t.\t.\t353.46\t370.46\t.\t.\t.\t.\t.\t.\t.\t.\t140.47\t344.61\t216.62\t286.09\t192.19\t258.79\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t197.25\t191.65\t.\t.\t.\t.\t147.3\t115.12\t.\t.\t185.4\t210.3\t251.58\t186.42\t357.39\t181.16\t149.78\t154.5\t.\t.\t.\t.\t.\t.\t.\t.\n+A_92_P033825\t460.01\t128.24\t.\t.\t.\t.\t.\t.\t385.1\t258.97\t282.39\t281.72\t206.93\t165.61\t.\t.\t347.97\t287.25\t486.98\t176.54\t504.52\t231.28\t440.25\t493.77\t.\t.\t261.87\t222.4\t.\t.\t.\t.\t.\t.\t229.58\t236.71\t376.18\t703.23\t.\t.\t376.81\t367.17\t387.15\t248.84\t.\t.\t413.74\t500.88\t.\t.\t360.97\t305.31\t.\t.\t.\t.\t311.41\t246.04\t.\t.\t231.03\t351.79\t342.72\t190.26\t.\t.\t.\t.\t476.53\t604.23\t.\t.\t271.85\t215.69\t460.8\t345.12\t195.13\t370.41\t137.71\t343.67\t389.96\t227.93\t372.47\t368.99\t472.79\t241.56\t.\t.\t599.42\t193\t504.23\t121.57\t479.63\t207.87\t.\t.\t338.52\t95.3\t373.02\t187.95\n+A_92_P033667\t386.52\t423.89\t.\t.\t760.15\t2548.5\t310.82\t574.12\t1438.53\t841.69\t540.84\t1875.51\t449.64\t438.69\t.\t.\t1417.45\t453.52\t381.67\t550.13\t330.72\t887.46\t512.81\t811.82\t1170.94\t1488.12\t1150.07\t414.99\t.\t.\t.\t.\t1710.5\t2146.07\t2461.97\t348.85\t586.63\t3412.57\t1500.59\t348.25\t494.78\t622.03\t350.67\t326.21\t2471.09\t1228.41\t494.27\t870.66\t971.27\t352.28\t534.69\t2001.7\t352.18\t1310.25\t472.15\t2623.92\t411.2\t2910.29\t1750.46\t322.42\t1317.96\t1445.15\t860.99\t311.84\t275.49\t166.4\t.\t.\t1115.92\t1497.93\t1546.84\t429.84\t711.39\t282.58\t1157.34\t700.96\t1586.29\t1498.68\t270.74\t353.16\t246.42\t1194.49\t981.74\t508.37\t1330.64\t330.45\t430.53\t285.33\t598.13\t328.11\t459.56\t1110.11\t710.93\t303.52\t493.69\t447.03\t504.11\t266.38\t346.4\t1700.61\n+-stop traits\n+-quit\n+-end\n' |
| b |
| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/input/qtlcart6.inp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/input/qtlcart6.inp Fri Mar 18 05:51:39 2016 -0400 |
| b |
| b'@@ -0,0 +1,692 @@\n+#bycross\n+-SampleSize 100\n+-Cross Ri1\n+-traits 4\n+-otraits 0\n+-missingtrait .\n+-case yes\n+-TranslationTable\n+AA\t2\tA\n+Aa\t1\t*1\n+aa\t0\tB\n+A-\t12\t*2\n+a-\t10\t*3\n+--\t-1\t-\n+-start markers\n+phi056 A A B B A B B A A A B A B A A A A A A A A A B A \n+B B A B - B B A B B - - A B A B A - - A B A A A A B A A A - B A B B - \n+A - B B B B A B A B A B - - A B A B A - B A A A A B A A B A B A A B A \n+B A B A A B \n+bnl5.62 A A - B A B B A B A B A B B A A A A A A A A B A \n+B A - B - A A A B A - A A B A B A B A A B A A A - B A A A B B A B B - \n+A A B B B B A B A B A A A - A B A B B A B A A - A B A A B A B B A B A \n+B A B A A B \n+umc1041 A A B B A A B A B B A B B A - A B A A A A B B A \n+A A B B - A A A B A B B B B B A - B A A B A A A - A A B - - B A B B B \n+A A B A B A A B A B A A A B A B A B A A B A - A A B A A B A B A A A A \n+B A B B A B \n+umc157a A A B A B A B A A B B - B A A A B - B A A A A A \n+A B B B - A A A B A A A B B A A B B B A A - B A A B A B A A B A A B B \n+A A B A B A A B B A A A A B A B B A B A A A A B A A B A B A B B A B A \n+B A B B B B \n+bnlg1178 A A A A B A B A A B B - B B A A B B B A A B A A \n+A B B B B A A A B A A A B B A A B B B A A - B A B - A B - A A - A B - \n+A A B A A A A B A A A A B B A - A A B B A A A B A A B - B - B B A B A \n+B A B B B B \n+bnlg1429 A A A A B A B A A B B B B B A A B - B A A B A A \n+A B B B B A A A B A A A B B A A B A B A A - B A B B A B - - A A B B - \n+B A B A A A A B A A A A A B A - A A B A A A A B A A B A B A A B A B A \n+B A B B B B \n+bnlg1627 A A A A B B A A B B A B B A A A B B B A A B A A \n+A B - B B A A A B A A A B B A A B A B A A - B A B B A B B - - A B B - \n+A A B A A A A B A B A A A B A B A A B A A A A B A A B A A A A B A B A \n+A A B B B B \n+umc11a A A - A B B B A B B A A B A A B B B B A A A - B \n+A B B B A B A A B B B A B B B A B A B A A B B A B - B B A B A B A B B \n+A A B B A A A B - B A A A B A B B A B A B - A B A A B B A B B - A B A \n+B A B B B B \n+bnlg439 A A A A B B A A B B A A - A A B B B B A A A B B \n+A B A B A A A A B B B A B B B B A A B A A B A B B - - B A B A B A B B \n+A B B A A A A B - B B A B B A - B B B B A A A B A - B A B B B - B - A \n+A A B B B B \n+bnlg2238 A A A - B B A A B B A B A A A B B A A A A A A B \n+A B A B A A A A B B B A A B B A A A - A A B A B B A A B A B A B - B B \n+A B B B A A A B B B B A A B A B B B B A A - A A A A A A A A A A B A A \n+A A - B B B \n+Bnlg1811_U A A A B B A A B B B B B A A A A B A A A A A A B \n+A B A B B B A A B B A A A B B A B A A A B B B B A A B B A B A B A B B \n+A B B B A A A B B B B A A B A B B B B A A A A B - B A B B B A A B A A \n+A A B B A B \n+bnlg2086 A B A A A A A A B B B B A A B - B A A B A A A B \n+A B A B B B A A B A B A A B B B B A A B B - A B B A B B A B B B A B B \n+B B B B A A A B B B A A A B B B - B B A - A A B B A A B B B A A B A A \n+A A A B A B \n+csu61b B B - A B A A A B B B B A B A - B B B B - B A B \n+B A A B B A A A B A B A A B B B B A - B A A - B - B B B A B B B A B B \n+A B B A A A A B B B A B A B A B - B B A - - A B A A - B B B A - B - A \n+A A B B A B \n+bnlg1057 B B A A A A B A B B B B A B A - B B A B B B B B \n+A B A B B A A A - A B A A B B B A A - A A A - B A - B B A - B B A B B \n+A B - A A A A - B A A B A B A B A B B A - B A B A A - B B B A - B - A \n+A A B B A B \n+umc1122 A B A A B A B A B B A B B B A A A B A B A B B A \n+B B A B B B A A B A B A A B B B A A B A A A B B A B B A A A B A A B A \n+A B A A A A B A B A B B A B A B A B B A A A B B A B B B B B B B B B B \n+A A B A A B \n+Bnlg615_U A A B A B B A A B A A B A B A B A B A A A B B B \n+B A A A B A A B B B B A A B B B A A B A A B B B A B B A A - B - A B A \n+A A B A B A B B B A B B A B - B A B B A A A B A A B B B A B B B B B B \n+A A B A A B \n+umc1128 A B B A B B B B B B B A A B A B A B A B A B B A \n+A A B A B A A B B B B A A B B B A A B A A B B B '..b' B A B - A B A B A B A B A - A A B A B A B B B B - \n+A B B A A A \n+umc1115 A B B B A B A A A B B B A B A A A A B A A A A B \n+B A A A B B B A A B A B - A B A A B - B A B A A A A A A B A A A A A B \n+A B A A B A A A B A B A A A B B A A B A B A A A A A A A B A A A A A A \n+B B B A A A \n+npi232a A B A B A B B A A B B B A B A A A A A A A A A B \n+B A A A B B B A A B A B B A B B A B A B A A A B A A A A B A A A A A B \n+A B A A A A A A B A B A A A B B A A A A A A A A A A A A A A A A A A A \n+B A B A A A \n+umc44a A B A B A B B A A B B B B B A A A A A A A A A B \n+B A B A B A B A A - B B A A B A A B A B A A A A - A - A B A B A A - B \n+A B A A A A A B B A A A A A A B A A A A A A A A A A A A A - B A A A A \n+B B B A A A \n+umc182 B B A B A B B A A B B B B B A A B A A B B A A B \n+A A B A B A B A B B B B B A B A A B A B A - A A B A B A B A B A A - B \n+A B B A A B A B B A A A A A A B A B A A A B A A A A A B A B B B A A A \n+B B B A B A \n+bnlg236 B A A B A B A A A B B A B B A A A A A B B A A B \n+A A B A B B B A B B B B B A B A A B A B A A A B B A B A B B B A A A B \n+A B B A A A A B B A A A A A A B A B A A A B A B A - A B A B B A A A A \n+A B B A B A \n+bnl7.49a B A - B B A A - A A A - A B A A A A A B B A A B \n+A - B A B B - A A B B B - B B A A A A A A - A B B A B A B B B A A - B \n+B A A A A B A A B A B A A A A B A B A A B - A - A B - B - B B - A A A \n+A B B A B A \n+bnlg1450 A A A B A B A A A B - A A B A B A A A B A A A B \n+A B B - A B B A A B B B B B B A A B A A A - A A B A B A B A B A B - B \n+B B A B A B A A - A B A B A B B A B A B B A A B A A A B A B B A B A A \n+A B A A B A \n+umc1038 A A A B B B A B B B B A B A A B A A A B A B A B \n+A B B B A A A A B A B B B - A A - A - B A B B A B B B A B A B A B - B \n+B B B B A B A B A A B A - A B B B B A B A A B B A A A B - B A B B B A \n+A B A A B - \n+-stop markers\n+-start traits\n+A_92_P033184\t.\t.\t.\t.\t166.33\t218.68\t.\t.\t.\t.\t237.31\t207.1\t171.89\t223.16\t.\t.\t148.1\t178.22\t147.72\t207.93\t234.15\t283.15\t216.04\t204.9\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t548.56\t286.64\t.\t.\t.\t.\t243.28\t279.47\t.\t.\t243.22\t287.6\t304.56\t248.28\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t205.54\t221.5\t.\t.\t.\t.\t.\t.\t.\t.\t164.7\t159.57\t.\t.\t.\t.\t181.96\t163.49\t235.93\t323.77\t273.08\t194.07\t101.96\t122.38\t277.79\t205.98\t.\t.\t.\t.\t.\t.\n+A_92_P033019\t.\t.\t.\t.\t.\t.\t.\t.\t163.33\t126.98\t173.51\t165.86\t177.55\t212.33\t.\t.\t186.65\t166.35\t215.29\t189.56\t290.38\t278.95\t193.22\t275.96\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t453.86\t281.25\t.\t.\t188.52\t226.4\t.\t.\t212.14\t190.59\t.\t.\t338.5\t295.84\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t228.28\t240.18\t.\t.\t.\t.\t174.16\t198.78\t.\t.\t165.81\t183.59\t.\t.\t.\t.\t.\t.\t.\t.\t295.24\t222.68\t143.64\t167.87\t.\t.\t.\t.\t.\t.\t.\t.\n+A_92_P032694\t1377.96\t1115.9\t.\t.\t1616.26\t152.45\t.\t.\t149.88\t1610.87\t1531.98\t137.24\t1123.09\t564.28\t691.3\t353.03\t106.04\t684.61\t189.87\t179.34\t972.15\t197.13\t611.54\t793.63\t.\t.\t889.86\t1394.75\t862.36\t871.54\t.\t.\t625.28\t136.65\t2592.04\t1814.04\t192.96\t222.4\t.\t.\t1050.62\t133.15\t236.41\t177.52\t.\t.\t311.18\t1873.33\t.\t.\t.\t.\t2011.22\t483.36\t338.56\t1063.01\t739.29\t799.97\t298.91\t2061.62\t.\t.\t786.08\t323.81\t.\t.\t.\t.\t663.9\t1172.39\t142.82\t1131.35\t.\t.\t309.76\t200.44\t281.29\t136.37\t867.13\t1367.14\t.\t.\t.\t.\t3179\t156.91\t770.79\t172.68\t1574.52\t137.67\t147.55\t112.18\t314.02\t147\t.\t.\t.\t.\t897.44\t174.92\n+A_92_P032375\t1134.65\t894.22\t574.07\t1104.6\t657.31\t623.14\t566.85\t856.48\t815.8\t775.59\t876.4\t459.67\t659.55\t846.53\t597.96\t415.41\t593.95\t1060.15\t857.23\t958.86\t905.95\t1671\t759.88\t1190.89\t833.52\t753.98\t750.53\t1098.17\t491.81\t869.72\t548.4\t542.42\t310.74\t359.28\t676.08\t650.38\t775.59\t1343.33\t616.86\t498.33\t947.64\t808.52\t1234.17\t562.74\t602.26\t1143.37\t903.77\t919.29\t718.84\t1056.67\t1290.09\t767.21\t849.67\t927.37\t559.44\t1016.14\t935.32\t531.78\t798.28\t647.51\t876.68\t655.22\t754.62\t452.87\t320.8\t249.69\t.\t.\t1067.54\t1255.88\t781.35\t797.5\t518.23\t374.25\t599.63\t505.13\t984.11\t613.4\t627.51\t527.93\t1031.59\t643.56\t1304.58\t740.71\t1021.57\t754.4\t1023.7\t496.3\t1771.62\t769.57\t1105.97\t468.27\t1686.62\t670.37\t811.16\t689.38\t1375.6\t663.67\t1006.37\t708.56\n+-stop traits\n+-quit\n+-end\n' |
| b |
| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/input/qtlcart7.inp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/input/qtlcart7.inp Fri Mar 18 05:51:39 2016 -0400 |
| b |
| b'@@ -0,0 +1,692 @@\n+#bycross\n+-SampleSize 100\n+-Cross Ri1\n+-traits 4\n+-otraits 0\n+-missingtrait .\n+-case yes\n+-TranslationTable\n+AA\t2\tA\n+Aa\t1\t*1\n+aa\t0\tB\n+A-\t12\t*2\n+a-\t10\t*3\n+--\t-1\t-\n+-start markers\n+phi056 A A B B A B B A A A B A B A A A A A A A A A B A \n+B B A B - B B A B B - - A B A B A - - A B A A A A B A A A - B A B B - \n+A - B B B B A B A B A B - - A B A B A - B A A A A B A A B A B A A B A \n+B A B A A B \n+bnl5.62 A A - B A B B A B A B A B B A A A A A A A A B A \n+B A - B - A A A B A - A A B A B A B A A B A A A - B A A A B B A B B - \n+A A B B B B A B A B A A A - A B A B B A B A A - A B A A B A B B A B A \n+B A B A A B \n+umc1041 A A B B A A B A B B A B B A - A B A A A A B B A \n+A A B B - A A A B A B B B B B A - B A A B A A A - A A B - - B A B B B \n+A A B A B A A B A B A A A B A B A B A A B A - A A B A A B A B A A A A \n+B A B B A B \n+umc157a A A B A B A B A A B B - B A A A B - B A A A A A \n+A B B B - A A A B A A A B B A A B B B A A - B A A B A B A A B A A B B \n+A A B A B A A B B A A A A B A B B A B A A A A B A A B A B A B B A B A \n+B A B B B B \n+bnlg1178 A A A A B A B A A B B - B B A A B B B A A B A A \n+A B B B B A A A B A A A B B A A B B B A A - B A B - A B - A A - A B - \n+A A B A A A A B A A A A B B A - A A B B A A A B A A B - B - B B A B A \n+B A B B B B \n+bnlg1429 A A A A B A B A A B B B B B A A B - B A A B A A \n+A B B B B A A A B A A A B B A A B A B A A - B A B B A B - - A A B B - \n+B A B A A A A B A A A A A B A - A A B A A A A B A A B A B A A B A B A \n+B A B B B B \n+bnlg1627 A A A A B B A A B B A B B A A A B B B A A B A A \n+A B - B B A A A B A A A B B A A B A B A A - B A B B A B B - - A B B - \n+A A B A A A A B A B A A A B A B A A B A A A A B A A B A A A A B A B A \n+A A B B B B \n+umc11a A A - A B B B A B B A A B A A B B B B A A A - B \n+A B B B A B A A B B B A B B B A B A B A A B B A B - B B A B A B A B B \n+A A B B A A A B - B A A A B A B B A B A B - A B A A B B A B B - A B A \n+B A B B B B \n+bnlg439 A A A A B B A A B B A A - A A B B B B A A A B B \n+A B A B A A A A B B B A B B B B A A B A A B A B B - - B A B A B A B B \n+A B B A A A A B - B B A B B A - B B B B A A A B A - B A B B B - B - A \n+A A B B B B \n+bnlg2238 A A A - B B A A B B A B A A A B B A A A A A A B \n+A B A B A A A A B B B A A B B A A A - A A B A B B A A B A B A B - B B \n+A B B B A A A B B B B A A B A B B B B A A - A A A A A A A A A A B A A \n+A A - B B B \n+Bnlg1811_U A A A B B A A B B B B B A A A A B A A A A A A B \n+A B A B B B A A B B A A A B B A B A A A B B B B A A B B A B A B A B B \n+A B B B A A A B B B B A A B A B B B B A A A A B - B A B B B A A B A A \n+A A B B A B \n+bnlg2086 A B A A A A A A B B B B A A B - B A A B A A A B \n+A B A B B B A A B A B A A B B B B A A B B - A B B A B B A B B B A B B \n+B B B B A A A B B B A A A B B B - B B A - A A B B A A B B B A A B A A \n+A A A B A B \n+csu61b B B - A B A A A B B B B A B A - B B B B - B A B \n+B A A B B A A A B A B A A B B B B A - B A A - B - B B B A B B B A B B \n+A B B A A A A B B B A B A B A B - B B A - - A B A A - B B B A - B - A \n+A A B B A B \n+bnlg1057 B B A A A A B A B B B B A B A - B B A B B B B B \n+A B A B B A A A - A B A A B B B A A - A A A - B A - B B A - B B A B B \n+A B - A A A A - B A A B A B A B A B B A - B A B A A - B B B A - B - A \n+A A B B A B \n+umc1122 A B A A B A B A B B A B B B A A A B A B A B B A \n+B B A B B B A A B A B A A B B B A A B A A A B B A B B A A A B A A B A \n+A B A A A A B A B A B B A B A B A B B A A A B B A B B B B B B B B B B \n+A A B A A B \n+Bnlg615_U A A B A B B A A B A A B A B A B A B A A A B B B \n+B A A A B A A B B B B A A B B B A A B A A B B B A B B A A - B - A B A \n+A A B A B A B B B A B B A B - B A B B A A A B A A B B B A B B B B B B \n+A A B A A B \n+umc1128 A B B A B B B B B B B A A B A B A B A B A B B A \n+A A B A B A A B B B B A A B B B A A B A A B B B '..b' A B A B A A A B B A A A A A A A A A A A A A A A A A A A \n+B A B A A A \n+umc44a A B A B A B B A A B B B B B A A A A A A A A A B \n+B A B A B A B A A - B B A A B A A B A B A A A A - A - A B A B A A - B \n+A B A A A A A B B A A A A A A B A A A A A A A A A A A A A - B A A A A \n+B B B A A A \n+umc182 B B A B A B B A A B B B B B A A B A A B B A A B \n+A A B A B A B A B B B B B A B A A B A B A - A A B A B A B A B A A - B \n+A B B A A B A B B A A A A A A B A B A A A B A A A A A B A B B B A A A \n+B B B A B A \n+bnlg236 B A A B A B A A A B B A B B A A A A A B B A A B \n+A A B A B B B A B B B B B A B A A B A B A A A B B A B A B B B A A A B \n+A B B A A A A B B A A A A A A B A B A A A B A B A - A B A B B A A A A \n+A B B A B A \n+bnl7.49a B A - B B A A - A A A - A B A A A A A B B A A B \n+A - B A B B - A A B B B - B B A A A A A A - A B B A B A B B B A A - B \n+B A A A A B A A B A B A A A A B A B A A B - A - A B - B - B B - A A A \n+A B B A B A \n+bnlg1450 A A A B A B A A A B - A A B A B A A A B A A A B \n+A B B - A B B A A B B B B B B A A B A A A - A A B A B A B A B A B - B \n+B B A B A B A A - A B A B A B B A B A B B A A B A A A B A B B A B A A \n+A B A A B A \n+umc1038 A A A B B B A B B B B A B A A B A A A B A B A B \n+A B B B A A A A B A B B B - A A - A - B A B B A B B B A B A B A B - B \n+B B B B A B A B A A B A - A B B B B A B A A B B A A A B - B A B B B A \n+A B A A B - \n+-stop markers\n+-start traits\n+A_92_P031891\t.\t.\t185.07\t210.53\t.\t.\t.\t.\t327.43\t159.35\t179.27\t144.93\t.\t.\t.\t.\t142.12\t162.29\t218.97\t274.02\t202.63\t235.52\t278.46\t203.72\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t210.8\t269.65\t190.55\t170.9\t171.33\t164.23\t157.52\t170.12\t158.75\t177.98\t.\t.\t375.52\t290.97\t.\t.\t234.98\t202.59\t.\t.\t.\t.\t216.82\t214.52\t160.04\t159.56\t207.31\t137.82\t.\t.\t.\t.\t.\t.\t238.08\t244.75\t281.89\t301.01\t.\t.\t.\t.\t241.75\t170.53\t180.12\t218.28\t167.42\t122.86\t215.6\t198.4\t345.74\t198.48\t.\t.\t277.58\t218.88\t123.44\t131.5\t196.57\t168.98\t270.68\t202.77\t.\t.\t212.95\t254.99\n+A_92_P031571\t.\t.\t.\t.\t.\t.\t149.06\t143.88\t.\t.\t257.66\t274.23\t204.51\t262.85\t221.08\t248.5\t151.77\t180.6\t128.64\t225.32\t459.37\t253.45\t145.95\t169.98\t.\t.\t.\t.\t231.86\t177.57\t.\t.\t.\t.\t.\t.\t.\t.\t158.25\t167.06\t270.22\t313.46\t.\t.\t.\t.\t370.67\t225.15\t.\t.\t.\t.\t.\t.\t.\t.\t276.73\t130.86\t192.35\t222.65\t.\t.\t230.39\t289.03\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t154.78\t129.06\t152.47\t173.05\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t241.3\t298.94\t124.84\t103.4\t.\t.\t206.59\t336.19\t179.65\t311.31\t160.74\t146.89\n+A_92_P031411\t738.56\t987.27\t887.79\t749.39\t640.53\t588.17\t788.51\t839.03\t856.18\t782.37\t953.48\t803.57\t826.65\t721.51\t735.18\t629.99\t927.8\t1050.1\t1132.63\t1263.21\t1512.06\t1331.39\t1275.2\t1102.96\t702.46\t921.14\t648.82\t822.3\t652.56\t745.59\t721.26\t806.86\t278.95\t291.98\t643.35\t819.69\t1021.47\t771.86\t804.92\t941.93\t929.73\t1136.91\t355.19\t606.82\t1016.27\t1017.32\t954.17\t849.71\t693.51\t521.92\t764.52\t725.66\t743.35\t835.42\t806.67\t815.68\t735.19\t694.57\t956.09\t695.86\t669.36\t601.84\t671.98\t680.31\t194.76\t200.44\t.\t.\t989.7\t938.98\t994.14\t951.8\t650.96\t496.21\t777.7\t872.15\t559.5\t991.57\t870.76\t888.03\t602.02\t569.34\t582\t900.97\t643.69\t751.52\t746.95\t722.74\t569.54\t775.7\t683.56\t840.33\t765.62\t888.29\t840.63\t796.36\t547.97\t653.45\t792.12\t769.1\n+A_92_P030934\t6951.26\t11060.57\t12533.99\t10285.3\t9427.41\t12483.79\t9209.6\t13099.35\t10388.85\t9397.54\t.\t.\t9965.92\t9921.26\t11871.55\t10470.17\t10393.34\t12890.02\t12927.17\t12743.03\t19592.33\t23209.15\t15167.41\t13445.38\t12226.61\t10085.63\t9484.12\t11619.39\t12024.29\t11020.13\t16835.25\t10841.71\t8550.85\t9891.16\t12704.62\t13684.77\t15412.64\t7233.72\t7654.85\t8656.68\t11370.89\t15410.39\t5872.32\t6501.74\t16219.14\t14098.27\t15159.9\t9893.28\t13092.57\t10789.81\t9352.48\t10878.85\t14681.64\t10648.02\t12209.18\t14703.78\t12843.73\t8932.25\t11260.67\t10904.77\t9670.74\t8504.76\t11346.75\t15032.62\t3359.44\t3985.33\t922.95\t1359.54\t13043.65\t13763.11\t15060.93\t11355.18\t8154.99\t8693.64\t9222.46\t9800.6\t6683.05\t10234.55\t13796.89\t9883.7\t8948.99\t9289.39\t8801.13\t11631.27\t9707.18\t11507.83\t10621.46\t10517.25\t8636.32\t13597.73\t10852.24\t11004.37\t11172.04\t12898.65\t11266.46\t16163.12\t14694.95\t11863.12\t11884.31\t8561.23\n+-stop traits\n+-quit\n+-end\n' |
| b |
| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/input/qtlcart8.inp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/input/qtlcart8.inp Fri Mar 18 05:51:39 2016 -0400 |
| b |
| b'@@ -0,0 +1,692 @@\n+#bycross\n+-SampleSize 100\n+-Cross Ri1\n+-traits 4\n+-otraits 0\n+-missingtrait .\n+-case yes\n+-TranslationTable\n+AA\t2\tA\n+Aa\t1\t*1\n+aa\t0\tB\n+A-\t12\t*2\n+a-\t10\t*3\n+--\t-1\t-\n+-start markers\n+phi056 A A B B A B B A A A B A B A A A A A A A A A B A \n+B B A B - B B A B B - - A B A B A - - A B A A A A B A A A - B A B B - \n+A - B B B B A B A B A B - - A B A B A - B A A A A B A A B A B A A B A \n+B A B A A B \n+bnl5.62 A A - B A B B A B A B A B B A A A A A A A A B A \n+B A - B - A A A B A - A A B A B A B A A B A A A - B A A A B B A B B - \n+A A B B B B A B A B A A A - A B A B B A B A A - A B A A B A B B A B A \n+B A B A A B \n+umc1041 A A B B A A B A B B A B B A - A B A A A A B B A \n+A A B B - A A A B A B B B B B A - B A A B A A A - A A B - - B A B B B \n+A A B A B A A B A B A A A B A B A B A A B A - A A B A A B A B A A A A \n+B A B B A B \n+umc157a A A B A B A B A A B B - B A A A B - B A A A A A \n+A B B B - A A A B A A A B B A A B B B A A - B A A B A B A A B A A B B \n+A A B A B A A B B A A A A B A B B A B A A A A B A A B A B A B B A B A \n+B A B B B B \n+bnlg1178 A A A A B A B A A B B - B B A A B B B A A B A A \n+A B B B B A A A B A A A B B A A B B B A A - B A B - A B - A A - A B - \n+A A B A A A A B A A A A B B A - A A B B A A A B A A B - B - B B A B A \n+B A B B B B \n+bnlg1429 A A A A B A B A A B B B B B A A B - B A A B A A \n+A B B B B A A A B A A A B B A A B A B A A - B A B B A B - - A A B B - \n+B A B A A A A B A A A A A B A - A A B A A A A B A A B A B A A B A B A \n+B A B B B B \n+bnlg1627 A A A A B B A A B B A B B A A A B B B A A B A A \n+A B - B B A A A B A A A B B A A B A B A A - B A B B A B B - - A B B - \n+A A B A A A A B A B A A A B A B A A B A A A A B A A B A A A A B A B A \n+A A B B B B \n+umc11a A A - A B B B A B B A A B A A B B B B A A A - B \n+A B B B A B A A B B B A B B B A B A B A A B B A B - B B A B A B A B B \n+A A B B A A A B - B A A A B A B B A B A B - A B A A B B A B B - A B A \n+B A B B B B \n+bnlg439 A A A A B B A A B B A A - A A B B B B A A A B B \n+A B A B A A A A B B B A B B B B A A B A A B A B B - - B A B A B A B B \n+A B B A A A A B - B B A B B A - B B B B A A A B A - B A B B B - B - A \n+A A B B B B \n+bnlg2238 A A A - B B A A B B A B A A A B B A A A A A A B \n+A B A B A A A A B B B A A B B A A A - A A B A B B A A B A B A B - B B \n+A B B B A A A B B B B A A B A B B B B A A - A A A A A A A A A A B A A \n+A A - B B B \n+Bnlg1811_U A A A B B A A B B B B B A A A A B A A A A A A B \n+A B A B B B A A B B A A A B B A B A A A B B B B A A B B A B A B A B B \n+A B B B A A A B B B B A A B A B B B B A A A A B - B A B B B A A B A A \n+A A B B A B \n+bnlg2086 A B A A A A A A B B B B A A B - B A A B A A A B \n+A B A B B B A A B A B A A B B B B A A B B - A B B A B B A B B B A B B \n+B B B B A A A B B B A A A B B B - B B A - A A B B A A B B B A A B A A \n+A A A B A B \n+csu61b B B - A B A A A B B B B A B A - B B B B - B A B \n+B A A B B A A A B A B A A B B B B A - B A A - B - B B B A B B B A B B \n+A B B A A A A B B B A B A B A B - B B A - - A B A A - B B B A - B - A \n+A A B B A B \n+bnlg1057 B B A A A A B A B B B B A B A - B B A B B B B B \n+A B A B B A A A - A B A A B B B A A - A A A - B A - B B A - B B A B B \n+A B - A A A A - B A A B A B A B A B B A - B A B A A - B B B A - B - A \n+A A B B A B \n+umc1122 A B A A B A B A B B A B B B A A A B A B A B B A \n+B B A B B B A A B A B A A B B B A A B A A A B B A B B A A A B A A B A \n+A B A A A A B A B A B B A B A B A B B A A A B B A B B B B B B B B B B \n+A A B A A B \n+Bnlg615_U A A B A B B A A B A A B A B A B A B A A A B B B \n+B A A A B A A B B B B A A B B B A A B A A B B B A B B A A - B - A B A \n+A A B A B A B B B A B B A B - B A B B A A A B A A B B B A B B B B B B \n+A A B A A B \n+umc1128 A B B A B B B B B B B A A B A B A B A B A B B A \n+A A B A B A A B B B B A A B B B A A B A A B B B '..b'A B B A A A A A A B A A A A A A A A A A A A A - B A A A A \n+B B B A A A \n+umc182 B B A B A B B A A B B B B B A A B A A B B A A B \n+A A B A B A B A B B B B B A B A A B A B A - A A B A B A B A B A A - B \n+A B B A A B A B B A A A A A A B A B A A A B A A A A A B A B B B A A A \n+B B B A B A \n+bnlg236 B A A B A B A A A B B A B B A A A A A B B A A B \n+A A B A B B B A B B B B B A B A A B A B A A A B B A B A B B B A A A B \n+A B B A A A A B B A A A A A A B A B A A A B A B A - A B A B B A A A A \n+A B B A B A \n+bnl7.49a B A - B B A A - A A A - A B A A A A A B B A A B \n+A - B A B B - A A B B B - B B A A A A A A - A B B A B A B B B A A - B \n+B A A A A B A A B A B A A A A B A B A A B - A - A B - B - B B - A A A \n+A B B A B A \n+bnlg1450 A A A B A B A A A B - A A B A B A A A B A A A B \n+A B B - A B B A A B B B B B B A A B A A A - A A B A B A B A B A B - B \n+B B A B A B A A - A B A B A B B A B A B B A A B A A A B A B B A B A A \n+A B A A B A \n+umc1038 A A A B B B A B B B B A B A A B A A A B A B A B \n+A B B B A A A A B A B B B - A A - A - B A B B A B B B A B A B A B - B \n+B B B B A B A B A A B A - A B B B B A B A A B B A A A B - B A B B B A \n+A B A A B - \n+-stop markers\n+-start traits\n+A_92_P030772\t362.91\t532.12\t869.78\t560\t826.16\t1255.2\t783.22\t538.78\t494.98\t516.79\t839.49\t679.53\t674.58\t1085.57\t.\t.\t798.15\t1283.23\t577.44\t401.84\t1583.4\t1275.88\t916.65\t680.26\t810.73\t583.75\t357.45\t491.88\t.\t.\t972.81\t771.83\t.\t.\t557.24\t684.74\t947.02\t289.15\t537.31\t504.76\t684.45\t1009.71\t266.15\t416.81\t585.45\t927.7\t969.76\t681.95\t623.35\t424.99\t337.52\t903.02\t825.78\t595.3\t554.3\t726.41\t907.32\t563.18\t704.37\t556.82\t402.6\t958.19\t669.67\t1127.31\t258.09\t391.04\t.\t.\t572.56\t541.57\t889.99\t675.79\t639.02\t525.87\t545.81\t765.85\t202\t935.73\t900.73\t563.48\t333.72\t799.05\t349.52\t660.89\t327.63\t830.38\t537.27\t750\t338.86\t771.56\t497.41\t647.82\t472.42\t878.01\t563.47\t951.99\t512.28\t750.12\t674.52\t569.36\n+A_92_P029803\t1507.68\t1869.05\t1646.63\t2791.27\t2083.07\t3707.69\t1528.52\t2433.06\t1726.4\t2045.43\t2662.08\t2144.67\t1823.96\t1843.79\t2455.67\t2874.57\t1938.55\t1857.31\t2643.25\t2374.17\t3154.55\t3956.89\t2046.15\t2717.33\t2124.09\t2399.96\t1938.19\t1957.74\t1571.5\t2709.33\t1929.12\t2418.53\t1858.47\t2298.42\t3687.13\t2289.15\t3697.06\t1703.62\t1480.12\t1746.6\t2176.05\t2893.21\t1249.91\t2171.55\t3329.72\t3366.38\t3121.6\t2468.93\t2146.27\t2085.06\t2185.23\t2326.29\t2731.6\t2312.37\t2267.85\t3203.33\t2221.77\t2731.24\t2630.3\t2495.55\t2082.69\t1872.13\t2265.52\t2139\t787.93\t833.07\t431.36\t633.26\t2311.77\t2306.35\t2092.11\t2323.09\t1856.88\t1362.83\t2946.86\t1996.59\t1349.5\t1953.98\t1954.35\t2214.44\t1951.61\t1692.47\t1398.89\t2443.11\t1832.01\t2458.35\t2361.76\t2036.73\t1479.48\t2599.47\t2145.55\t2456.2\t2595.75\t2483.22\t1830.7\t2519.62\t2421.19\t1834.01\t2333.72\t2253.46\n+A_92_P029488\t862.37\t372.91\t313.77\t684.99\t434.59\t444.57\t329.91\t590.74\t1239.85\t1127.16\t1389.61\t1035.24\t1435.6\t1037.43\t2203.97\t2450.9\t517.97\t656.47\t995.33\t1320.39\t1077.91\t1471.64\t749.78\t810.63\t1485.64\t1071.41\t1233.8\t1810.53\t.\t.\t1140.53\t1114.92\t887.76\t1318.95\t2203.63\t1203.1\t1255.29\t2169.8\t1197.97\t954.91\t1280.14\t865.73\t2037.35\t793.62\t1390.07\t1942.73\t2540.31\t1850.98\t949.68\t2212.55\t2399.56\t1122.88\t1740.22\t1115.89\t1442.84\t1450.92\t1719.63\t1067.22\t1393.68\t1224.62\t1199.74\t811.47\t2065.37\t1393.31\t814.52\t509.66\t335\t538.34\t1103.43\t1671.59\t1057.57\t1152.04\t680.89\t921.44\t1237.9\t1588.1\t1967.38\t777.18\t1293.93\t1452.74\t2126.45\t895.31\t2776.12\t1714.17\t2407.24\t1445.82\t2093.98\t1228.88\t1186.25\t857.43\t1980.22\t923\t2231.97\t881.11\t1272.6\t1947.58\t1834.22\t1159.26\t1138.03\t1413.23\n+A_92_P029164\t.\t.\t.\t.\t.\t.\t.\t.\t1646.66\t1861.7\t914.02\t1313.05\t.\t.\t.\t.\t142.71\t3932.66\t285.95\t402.73\t249.44\t10946.44\t2345.95\t3186.57\t3420.43\t154.18\t.\t.\t.\t.\t.\t.\t2408.5\t1191.72\t.\t.\t228.49\t1688.31\t854.74\t2230.37\t.\t.\t2525.4\t111.9\t211.25\t1898.25\t1835.6\t941.89\t.\t.\t.\t.\t.\t.\t2164.67\t5650.79\t.\t.\t.\t.\t6104.78\t2839.45\t.\t.\t447.17\t1299.26\t462.36\t393.22\t313.9\t5937.43\t945.96\t189.4\t745.22\t862.2\t2281.32\t118.4\t916.65\t1503.83\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t3908.26\t2806.93\t6162.17\t1037.44\t.\t.\t3607.46\t1728.56\t1185.99\t3003.31\n+-stop traits\n+-quit\n+-end\n' |
| b |
| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/input/qtlcart9.inp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/input/qtlcart9.inp Fri Mar 18 05:51:39 2016 -0400 |
| b |
| b'@@ -0,0 +1,692 @@\n+#bycross\n+-SampleSize 100\n+-Cross Ri1\n+-traits 4\n+-otraits 0\n+-missingtrait .\n+-case yes\n+-TranslationTable\n+AA\t2\tA\n+Aa\t1\t*1\n+aa\t0\tB\n+A-\t12\t*2\n+a-\t10\t*3\n+--\t-1\t-\n+-start markers\n+phi056 A A B B A B B A A A B A B A A A A A A A A A B A \n+B B A B - B B A B B - - A B A B A - - A B A A A A B A A A - B A B B - \n+A - B B B B A B A B A B - - A B A B A - B A A A A B A A B A B A A B A \n+B A B A A B \n+bnl5.62 A A - B A B B A B A B A B B A A A A A A A A B A \n+B A - B - A A A B A - A A B A B A B A A B A A A - B A A A B B A B B - \n+A A B B B B A B A B A A A - A B A B B A B A A - A B A A B A B B A B A \n+B A B A A B \n+umc1041 A A B B A A B A B B A B B A - A B A A A A B B A \n+A A B B - A A A B A B B B B B A - B A A B A A A - A A B - - B A B B B \n+A A B A B A A B A B A A A B A B A B A A B A - A A B A A B A B A A A A \n+B A B B A B \n+umc157a A A B A B A B A A B B - B A A A B - B A A A A A \n+A B B B - A A A B A A A B B A A B B B A A - B A A B A B A A B A A B B \n+A A B A B A A B B A A A A B A B B A B A A A A B A A B A B A B B A B A \n+B A B B B B \n+bnlg1178 A A A A B A B A A B B - B B A A B B B A A B A A \n+A B B B B A A A B A A A B B A A B B B A A - B A B - A B - A A - A B - \n+A A B A A A A B A A A A B B A - A A B B A A A B A A B - B - B B A B A \n+B A B B B B \n+bnlg1429 A A A A B A B A A B B B B B A A B - B A A B A A \n+A B B B B A A A B A A A B B A A B A B A A - B A B B A B - - A A B B - \n+B A B A A A A B A A A A A B A - A A B A A A A B A A B A B A A B A B A \n+B A B B B B \n+bnlg1627 A A A A B B A A B B A B B A A A B B B A A B A A \n+A B - B B A A A B A A A B B A A B A B A A - B A B B A B B - - A B B - \n+A A B A A A A B A B A A A B A B A A B A A A A B A A B A A A A B A B A \n+A A B B B B \n+umc11a A A - A B B B A B B A A B A A B B B B A A A - B \n+A B B B A B A A B B B A B B B A B A B A A B B A B - B B A B A B A B B \n+A A B B A A A B - B A A A B A B B A B A B - A B A A B B A B B - A B A \n+B A B B B B \n+bnlg439 A A A A B B A A B B A A - A A B B B B A A A B B \n+A B A B A A A A B B B A B B B B A A B A A B A B B - - B A B A B A B B \n+A B B A A A A B - B B A B B A - B B B B A A A B A - B A B B B - B - A \n+A A B B B B \n+bnlg2238 A A A - B B A A B B A B A A A B B A A A A A A B \n+A B A B A A A A B B B A A B B A A A - A A B A B B A A B A B A B - B B \n+A B B B A A A B B B B A A B A B B B B A A - A A A A A A A A A A B A A \n+A A - B B B \n+Bnlg1811_U A A A B B A A B B B B B A A A A B A A A A A A B \n+A B A B B B A A B B A A A B B A B A A A B B B B A A B B A B A B A B B \n+A B B B A A A B B B B A A B A B B B B A A A A B - B A B B B A A B A A \n+A A B B A B \n+bnlg2086 A B A A A A A A B B B B A A B - B A A B A A A B \n+A B A B B B A A B A B A A B B B B A A B B - A B B A B B A B B B A B B \n+B B B B A A A B B B A A A B B B - B B A - A A B B A A B B B A A B A A \n+A A A B A B \n+csu61b B B - A B A A A B B B B A B A - B B B B - B A B \n+B A A B B A A A B A B A A B B B B A - B A A - B - B B B A B B B A B B \n+A B B A A A A B B B A B A B A B - B B A - - A B A A - B B B A - B - A \n+A A B B A B \n+bnlg1057 B B A A A A B A B B B B A B A - B B A B B B B B \n+A B A B B A A A - A B A A B B B A A - A A A - B A - B B A - B B A B B \n+A B - A A A A - B A A B A B A B A B B A - B A B A A - B B B A - B - A \n+A A B B A B \n+umc1122 A B A A B A B A B B A B B B A A A B A B A B B A \n+B B A B B B A A B A B A A B B B A A B A A A B B A B B A A A B A A B A \n+A B A A A A B A B A B B A B A B A B B A A A B B A B B B B B B B B B B \n+A A B A A B \n+Bnlg615_U A A B A B B A A B A A B A B A B A B A A A B B B \n+B A A A B A A B B B B A A B B B A A B A A B B B A B B A A - B - A B A \n+A A B A B A B B B A B B A B - B A B B A A A B A A B B B A B B B B B B \n+A A B A A B \n+umc1128 A B B A B B B B B B B A A B A B A B A B A B B A \n+A A B A B A A B B B B A A B B B A A B A A B B B '..b' A A A B A B A A A B B A A A A A A A A A A A A A A A A A A A \n+B A B A A A \n+umc44a A B A B A B B A A B B B B B A A A A A A A A A B \n+B A B A B A B A A - B B A A B A A B A B A A A A - A - A B A B A A - B \n+A B A A A A A B B A A A A A A B A A A A A A A A A A A A A - B A A A A \n+B B B A A A \n+umc182 B B A B A B B A A B B B B B A A B A A B B A A B \n+A A B A B A B A B B B B B A B A A B A B A - A A B A B A B A B A A - B \n+A B B A A B A B B A A A A A A B A B A A A B A A A A A B A B B B A A A \n+B B B A B A \n+bnlg236 B A A B A B A A A B B A B B A A A A A B B A A B \n+A A B A B B B A B B B B B A B A A B A B A A A B B A B A B B B A A A B \n+A B B A A A A B B A A A A A A B A B A A A B A B A - A B A B B A A A A \n+A B B A B A \n+bnl7.49a B A - B B A A - A A A - A B A A A A A B B A A B \n+A - B A B B - A A B B B - B B A A A A A A - A B B A B A B B B A A - B \n+B A A A A B A A B A B A A A A B A B A A B - A - A B - B - B B - A A A \n+A B B A B A \n+bnlg1450 A A A B A B A A A B - A A B A B A A A B A A A B \n+A B B - A B B A A B B B B B B A A B A A A - A A B A B A B A B A B - B \n+B B A B A B A A - A B A B A B B A B A B B A A B A A A B A B B A B A A \n+A B A A B A \n+umc1038 A A A B B B A B B B B A B A A B A A A B A B A B \n+A B B B A A A A B A B B B - A A - A - B A B B A B B B A B A B A B - B \n+B B B B A B A B A A B A - A B B B B A B A A B B A A A B - B A B B B A \n+A B A A B - \n+-stop markers\n+-start traits\n+A_92_P029002\t429.65\t366.25\t468.78\t436.36\t380.34\t271.4\t283.01\t389.6\t484.17\t359.43\t412.19\t419.07\t425.52\t268.52\t.\t.\t344.13\t381.45\t510\t360.08\t586.55\t575.05\t577.04\t398.82\t.\t.\t320.58\t427.03\t.\t.\t.\t.\t482.97\t490.29\t513.3\t303.67\t498.6\t596.61\t591.27\t509.64\t475.68\t341.89\t392.44\t286.5\t685.94\t1061.29\t630.92\t653.97\t212.69\t395.38\t488.22\t260.61\t359.04\t336.68\t428.48\t403.54\t325.58\t480.31\t376.95\t466.59\t392.79\t443.58\t302.34\t253.51\t.\t.\t.\t.\t358.38\t452.06\t375.38\t482.5\t320.97\t293.88\t354.85\t461.38\t556.06\t374.57\t472.53\t457.82\t422.02\t302.82\t396.37\t379.9\t525.83\t579.42\t434.5\t340.72\t525.49\t412.65\t539.73\t399.2\t564.56\t444.97\t435.86\t486.86\t377.84\t312.87\t375.87\t432.77\n+A_92_P028842\t203.43\t278.08\t146.77\t241.75\t.\t.\t185.35\t240.55\t220.33\t247.77\t219.55\t227.77\t269.32\t179.27\t.\t.\t140.42\t279.56\t174.34\t174.9\t248.94\t278.4\t219.34\t336.09\t.\t.\t277\t189.29\t.\t.\t.\t.\t.\t.\t.\t.\t243.84\t289.59\t384.2\t158.94\t193.3\t212.36\t276.17\t177.59\t453.09\t545.47\t266.23\t285.56\t.\t.\t.\t.\t.\t.\t.\t.\t181.09\t267.63\t166.82\t294.71\t325.43\t145.2\t.\t.\t.\t.\t.\t.\t196.2\t318.07\t261.16\t273.23\t177.97\t197.41\t215.7\t122.59\t419.55\t186.13\t.\t.\t228.39\t137.62\t168.99\t131.72\t.\t.\t.\t.\t270.49\t227.11\t234.25\t178.39\t222.41\t197.24\t274.37\t181.97\t.\t.\t.\t.\n+A_92_P028354\t535.05\t519.58\t458.78\t718.73\t718.09\t500.31\t312.98\t339.61\t696.67\t576.64\t370.65\t653.07\t482.29\t324.88\t601.25\t665.53\t331.96\t498.21\t426.63\t550.71\t1099.57\t439.35\t656.13\t519.95\t335.9\t375.57\t663.62\t442.49\t726\t734.16\t.\t.\t.\t.\t837.53\t809.1\t307.34\t687.96\t938.48\t663.27\t327.66\t590.51\t732.21\t447.22\t603.42\t1008.87\t564.99\t748.7\t315.8\t675.04\t630.33\t320.15\t531.09\t370.98\t372.42\t510.47\t397.79\t632.83\t644.62\t598.79\t707.04\t490.57\t374.72\t372.68\t262.01\t171.09\t.\t.\t434.44\t514.02\t726.53\t278.31\t580.62\t353.12\t403.96\t455.08\t1240.46\t438.83\t324.06\t642.02\t694.18\t267.87\t610.75\t532.2\t1036.44\t833.27\t488.31\t474.61\t464.14\t455\t739.11\t413.01\t642.53\t678.35\t428.5\t506.48\t299.08\t217.55\t567.55\t766.83\n+A_92_P028042\t672.2\t581.52\t734\t640.4\t477.57\t392.32\t617.9\t783.12\t529.08\t485.62\t731.3\t441.44\t555.09\t645.07\t.\t.\t494.39\t982.64\t576.33\t636.07\t1152.67\t957.18\t1008.05\t648.11\t.\t.\t381.61\t604.75\t250.04\t493.76\t459.6\t525.16\t.\t.\t356.2\t633.97\t768.08\t582.57\t512.51\t564.81\t602.64\t849.56\t457.76\t476.35\t545.32\t678.45\t600.97\t614.59\t325.89\t411.03\t393.29\t297.9\t555.89\t505.81\t313.05\t508.52\t561.87\t325.16\t500.37\t495.4\t525.84\t347.54\t378.23\t538.49\t185.14\t255.54\t.\t.\t.\t.\t611.07\t706.2\t332.03\t375.7\t423.68\t613.88\t372.91\t437.45\t812.08\t549.87\t464.13\t335.66\t405.03\t518.77\t508.12\t607.98\t457.45\t305.68\t442.61\t600.65\t766.36\t457.72\t678.98\t623.95\t679.13\t740.87\t462.58\t417.28\t695.19\t337.66\n+-stop traits\n+-quit\n+-end\n' |
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| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/input/qtlcart_original.map.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/input/qtlcart_original.map.txt Fri Mar 18 05:51:39 2016 -0400 |
| [ |
| b'@@ -0,0 +1,251 @@\n+# 671562676 -filetype Rmap.out \n+#\n+#\tQTL Cartographer v. 1.17e, 27 August 2003\n+#\tThis output file (\\\\Trin.bi.up.ac.za\\duncan\\GLS_project\\Pipe_line\\MeQTL\\NewMcd01.map) was created by RMap...\n+#\n+#\tIt is 12:22:33 on Tuesday, 24 July 2012\n+#\n+#\n+#\n+# Here is the Map of Markers...\n+-s\n+-f 2 Map function [1,8]: Haldane is 1\n+-p 0.0000 Extra parameter for map functions [4-8]\n+-u c The units of measurement is centiMorgans.\n+#\n+# Markermap parameters\n+#\n+-c 10 Number of chromosomes.\n+-i 167 Total number of markers.\n+-m 16 Mean, and...\n+-vm 4.9001 ...standard deviation for Markers/Chromosome.\n+-d 11.8571 Mean, and...\n+-vd 6.0265 ...standard deviation for the intermarker distance.\n+-t -1.#IND Mean length of material outside the flanking markers.\n+#\n+ | Chromosome---->\n+--------------------------------------------------------------------------------------------\n+Marker | 1 2 3 4 5 6 7 8 9 10\n+--------------------------------------------------------------------------------------------\n+-l 0 | 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000\n+-l 1 | 7.5300 13.2700 11.7500 19.0000 3.2000 5.6200 9.0300 10.7400 17.9400 15.0200\n+-l 2 | 11.2400 26.0000 13.8400 10.5900 22.8200 8.9200 11.5700 14.7000 9.5600 17.5500\n+-l 3 | 19.9400 25.6300 16.5400 6.3400 7.5600 14.4900 10.2300 13.2900 18.4400 13.4800\n+-l 4 | 5.9100 17.1400 9.1100 17.1500 6.6500 6.8300 10.2300 11.4100 19.1100 6.9400\n+-l 5 | 4.1100 8.5600 10.0400 3.0800 9.6900 5.7300 4.1400 17.3300 27.0800 22.1800\n+-l 6 | 4.4800 10.4300 10.7400 14.0900 11.8600 19.4000 10.2400 15.8400 5.6800 6.3800\n+-l 7 | 16.7600 10.7100 6.1200 4.6300 15.4300 4.2800 7.7500 12.7700 22.7000 9.0700\n+-l 8 | 11.9000 5.3500 2.3600 17.3300 9.4900 6.4500 13.1400 3.2300 4.2700 8.0500\n+-l 9 | 14.2300 15.5300 22.9100 6.1700 7.7200 17.1500 11.3000 3.5800 15.6000 5.9300\n+-l 10 | 16.6000 8.8600 26.3700 12.9000 5.2800 26.9500 18.6800 15.3100 18.4000 13.0300\n+-l 11 | 14.1300 8.5600 7.0100 8.9700 11.4100 9.7400 4.8500 9.6600 0.0000 12.9000\n+-l 12 | 15.8600 16.2000 18.3000 7.6500 13.8900 13.8200 0.0000 3.1300 16.9500\n+-l 13 | 6.2800 2.8700 6.1200 9.7600 8.3200 20.3800 10.3200 0.0000\n+-l 14 | 15.3100 0.0000 16.3500 9.6600 7.7900 2.5400 0.0000 \n+-l 15 | 14.8400 10.9700 4.2500 23.2000 19.9200 \n+-l 16 | 8.1200 10.6200 17.0500 14.6200 13.6300 \n+-l 17 | 6.1800 14.4500 5.5800 11.9000 0.0000 \n+-l 18 | 8.7100 7.6900 9.1900 6.7100 \n+-l 19 | 33.9500 0.0000 4.9800 6.2800 \n+-l 20 | 19.7800 0.0000 0.0000 \n+-l 21 | 8.9400 \n+-l 22 | 10.2300 \n+-l 23 | 22.0600 \n+-l 24 | 3.1000 \n+-l 25 | 14.8400 \n+-l 26 | 9.3700 \n+-l 27 | 0.0000 \n+--------------------------------------------------------------------------------------------\n+-Number | 27 14 19 20 20 17 12 14 11 13\n+\n+\n+\n+Names and positions of the markers'..b' 2 bnl5.62\n+ 1 3 umc1041\n+ 1 4 umc157a\n+ 1 5 bnlg1178\n+ 1 6 bnlg1429\n+ 1 7 bnlg1627\n+ 1 8 umc11a\n+ 1 9 bnlg439\n+ 1 10 bnlg2238\n+ 1 11 Bnlg1811_U\n+ 1 12 bnlg2086\n+ 1 13 csu61b\n+ 1 14 bnlg1057\n+ 1 15 umc1122\n+ 1 16 Bnlg615_U\n+ 1 17 umc1128\n+ 1 18 umc166b\n+ 1 19 dupssr12\n+ 1 20 phi011\n+ 1 21 bnlg1720\n+ 1 22 umc106a\n+ 1 23 umc147b\n+ 1 24 umc1111_P\n+ 1 25 bnlg2331\n+ 1 26 bnlg2123\n+ 1 27 bnl6.32\n+ 2 1 phi402893\n+ 2 2 bnlg1297\n+ 2 3 bnlg2042\n+ 2 4 umc44b\n+ 2 5 csu40\n+ 2 6 umc135\n+ 2 7 csu54a\n+ 2 8 umc55a\n+ 2 9 umc14b\n+ 2 10 csu154a\n+ 2 11 umc150b\n+ 2 12 umc1551\n+ 2 13 umc36a\n+ 2 14 csu109a\n+ 3 1 umc32a\n+ 3 2 phi104127\n+ 3 3 bnlg1325\n+ 3 4 bnlg1447\n+ 3 5 umc92a\n+ 3 6 bnlg1019a\n+ 3 7 phi053\n+ 3 8 bnlg420\n+ 3 9 umc1307\n+ 3 10 Phi073_U\n+ 3 11 Bnlg1449_U\n+ 3 12 bnl10.24a\n+ 3 13 unknown1\n+ 3 14 umc3b\n+ 3 15 umc16a\n+ 3 16 bnlg1108_P\n+ 3 17 umc63a\n+ 3 18 bnlg1182\n+ 3 19 bnlg1754\n+ 4 1 umc1017\n+ 4 2 umc1294\n+ 4 3 phi021\n+ 4 4 umc1550\n+ 4 5 umc1652\n+ 4 6 bnlg490\n+ 4 7 csu100\n+ 4 8 umc156a\n+ 4 9 bnlg2291\n+ 4 10 umc19\n+ 4 11 mmc0341\n+ 4 12 umc133a\n+ 4 13 umc15a\n+ 4 14 csu11b\n+ 4 15 npi593a\n+ 4 16 bnlg589\n+ 4 17 umc1720_P\n+ 4 18 bnlg1337\n+ 4 19 phi019\n+ 4 20 phi006\n+ 5 1 bnl8.33\n+ 5 2 npi409\n+ 5 3 umc147a\n+ 5 4 umc90\n+ 5 5 umc107b\n+ 5 6 Bnlg105_U\n+ 5 7 bnlg1046\n+ 5 8 umc166a\n+ 5 9 bnl6.22\n+ 5 10 csu36b\n+ 5 11 DupSSR10_U\n+ 5 12 bnl5.71a\n+ 5 13 umc1155_P\n+ 5 14 npi237\n+ 5 15 umc54\n+ 5 16 bnlg1346\n+ 5 17 bnlg118\n+ 5 18 umc1225\n+ 5 19 umc104b\n+ 5 20 bnlg1885\n+ 6 1 umc85a\n+ 6 2 bnlg426\n+ 6 3 umc36c\n+ 6 4 umc1572_P\n+ 6 5 Bnlg2191_U\n+ 6 6 bnlg2151\n+ 6 7 umc1887\n+ 6 8 umc65a\n+ 6 9 umc1014\n+ 6 10 bnlg1922\n+ 6 11 umc1413_P\n+ 6 12 mmc0241\n+ 6 13 umc1424_P\n+ 6 14 umc36\n+ 6 15 umc39\n+ 6 16 bnlg1740\n+ 6 17 umc2059\n+ 7 1 csu13\n+ 7 2 bnlg1094\n+ 7 3 umc1393\n+ 7 4 bnlg1808\n+ 7 5 bnl15.21\n+ 7 6 bnlg339\n+ 7 7 bnlg155\n+ 7 8 bnlg1805\n+ 7 9 bnl14.07\n+ 7 10 umc1125\n+ 7 11 phi082\n+ 7 12 umc1799\n+ 8 1 npi114a\n+ 8 2 umc1327\n+ 8 3 npi110a\n+ 8 4 umc103a\n+ 8 5 bnlg669\n+ 8 6 umc1858\n+ 8 7 umc1562_P\n+ 8 8 umc48a\n+ 8 9 asg52a\n+ 8 10 umc150a\n+ 8 11 umc1384\n+ 8 12 umc7\n+ 8 13 bnlg1056\n+ 8 14 umc39b\n+ 9 1 bnlg1272\n+ 9 2 umc113a\n+ 9 3 umc1170_P\n+ 9 4 umc105a\n+ 9 5 umc81\n+ 9 6 bnl8.17\n+ 9 7 umc1231\n+ 9 8 umc1733\n+ 9 9 bnlg1588\n+ 9 10 bnlg1375\n+ 9 11 umc1137\n+ 10 1 phi118\n+ 10 2 npi285a\n+ 10 3 umc1337_P\n+ 10 4 umc130\n+ 10 5 bnlg1079\n+ 10 6 umc1115\n+ 10 7 npi232a\n+ 10 8 umc44a\n+ 10 9 umc182\n+ 10 10 bnlg236\n+ 10 11 bnl7.49a\n+ 10 12 bnlg1450\n+ 10 13 umc1038\n+-e MarkerNames\n+\n+\n+\n+Names of the Chromosomes\n+\n+-b ChromosomeNames \n+ 1 Ch1\n+ 2 Ch2\n+ 3 Ch3\n+ 4 Ch4\n+ 5 Ch5\n+ 6 Ch6\n+ 7 Ch7\n+ 8 Ch8\n+ 9 Ch9\n+ 10 Ch10\n+-e ChromosomeNames\n' |
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| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/output/qtl_out_1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/output/qtl_out_1.txt Fri Mar 18 05:51:39 2016 -0400 |
| b |
| @@ -0,0 +1,10 @@ +A_92_P039116 1 1 6 13 1.5339 15.9210885 3.4548762045 0.1919114 0.3879427 77.2994584 -311.3306014 0.0000000 13 1.4516 15 1.7163 13 1.4181 15 1.7956 +A_92_P039116 1 3 9 6 0.9214 15.3291347 3.3264222299 0.1176972 0.3098947 73.0022134 -249.9855214 0.0000000 5 0.8372 6 0.9652 5 0.7772 6 0.9724 +A_92_P039116 1 4 9 8 1.2052 13.9017110 3.016671287 0.1050450 0.3111284 71.1474755 245.1582644 0.0000000 7 1.2011 9 1.3362 7 1.1768 9 1.3935 +A_92_P038628 2 1 9 1 0.1601 24.5310019 5.3232274123 0.1989293 0.5098951 52.0670152 -701.7675097 0.0000000 1 0.0725 2 0.2239 1 0.0379 2 0.2472 +A_92_P038628 2 2 10 1 0.0201 12.8665772 2.7920472524 0.0951165 0.4914030 48.4981968 -480.0477241 0.0000000 1 0.0001 1 0.1196 1 0.0001 1 0.1444 +A_92_P038150 4 1 6 9 0.7773 13.7094809 2.9749573553 0.1131346 0.5435596 1.1541518 394.9822315 0.0000000 8 0.6819 9 0.8709 6 0.6046 9 0.8844 +A_92_P038150 4 2 9 9 1.2479 13.7334120 2.980150404 0.0784721 0.4919043 1.3007608 351.9779719 0.0000000 7 1.1444 9 1.3206 7 1.0201 9 1.3679 +A_92_P038150 4 3 10 2 0.1503 14.0299522 3.0444996274 0.0845627 0.4961190 1.2914158 342.6938285 0.0000000 1 0.0422 2 0.2273 1 0.0001 2 0.2856 +A_92_P038150 4 4 10 3 0.4058 15.3264104 3.3258310568 0.1320742 0.5272216 1.1053058 -483.3117444 0.0000000 3 0.3449 6 0.797 2 0.32 6 0.8084 +A_92_P038150 4 5 10 5 0.6500 39.1826820 8.502641994 0.3966235 0.5336773 19.1694948 -742.6937805 0.0000000 5 0.5749 5 0.7461 5 0.5467 5 0.7508 |
| b |
| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/output/qtl_out_10.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/output/qtl_out_10.txt Fri Mar 18 05:51:39 2016 -0400 |
| b |
| @@ -0,0 +1,10 @@ +A_92_P027554 1 1 2 13 1.6825 12.7611437 2.7691681829 0.1018072 0.3903601 4.4296057 167.8795132 0.0000000 12 1.5655 13 1.6825 11 1.4988 13 1.6825 +A_92_P027554 1 2 3 13 1.5510 20.3857124 4.4236995908 0.1619413 0.4031766 2.7686481 -211.1740827 0.0000000 12 1.4823 13 1.5956 12 1.4466 14 1.706 +A_92_P027554 1 4 10 4 0.4606 17.5002478 3.7975537726 0.1313607 0.3906483 3.3345446 -188.6856642 0.0000000 3 0.3584 4 0.5233 2 0.3245 5 0.6256 +A_92_P027390 2 1 6 8 0.6528 18.1173076 3.9314557492 0.2563745 0.6640015 0.4052638 47.1173201 0.0000000 6 0.5578 8 0.693 6 0.5159 8 0.7133 +A_92_P027390 2 2 6 12 1.3157 17.7087013 3.8427881821 0.3257878 0.6980663 0.4043924 -51.5935951 0.0000000 12 1.2576 12 1.3818 11 1.2481 12 1.3906 +A_92_P027072 3 2 7 11 1.1032 44.9795778 9.7605683826 0.2969825 0.5035042 4.6985714 1843.6463564 0.0000000 11 1.0867 11 1.1032 11 1.0772 11 1.1032 +A_92_P027072 3 3 9 8 1.2052 14.5812965 3.1641413405 0.0775113 0.5066064 4.4592073 985.5528170 0.0000000 7 1.1257 8 1.2359 7 1.0763 9 1.3895 +A_92_P026747 4 1 3 1 0.0401 24.1515872 5.2408944224 0.3905649 0.6410914 3.8219363 37.8546571 0.0000000 1 0.0081 1 0.1007 1 0.0001 1 0.1048 +A_92_P026747 4 2 3 9 0.8051 13.3190279 2.8902290543 0.1942427 0.5175014 30.0430325 -26.6445313 0.0000000 7 0.7614 9 0.9686 7 0.7247 9 1.0276 +A_92_P026747 4 3 6 5 0.3587 11.9666148 2.5967554116 0.1700650 0.5144391 28.6662391 25.6423152 0.0000000 3 0.2763 5 0.4027 3 0.1899 6 0.5236 |
| b |
| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/output/qtl_out_11.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/output/qtl_out_11.txt Fri Mar 18 05:51:39 2016 -0400 |
| b |
| @@ -0,0 +1,4 @@ +A_92_P025313 1 1 3 13 1.5510 20.6064068 4.4715902756 0.1710257 0.2747041 1109.4668897 -1905.2184858 0.0000000 12 1.5085 13 1.5862 12 1.4679 14 1.7055 +A_92_P024994 2 1 5 2 0.2121 17.4534281 3.7873938977 0.2637088 0.6641010 15.0444221 320.9327481 0.0000000 2 0.0364 3 0.2867 1 0.026 3 0.3122 +A_92_P024836 3 1 4 12 1.2626 14.9192368 3.2374743856 0.1173577 0.3739031 13.0708073 -100.1363730 0.0000000 11 1.143 13 1.3648 11 1.1137 14 1.4605 +A_92_P024836 3 2 8 8 0.9609 16.4094504 3.5608507368 0.1247620 0.3640049 12.1550179 111.8531092 0.0000000 7 0.8899 9 0.9997 7 0.8506 10 1.1185 |
| b |
| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/output/qtl_out_12.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/output/qtl_out_12.txt Fri Mar 18 05:51:39 2016 -0400 |
| b |
| @@ -0,0 +1,7 @@ +A_92_P024516 1 1 1 19 2.0214 20.5892047 4.4678574199 0.1627540 0.2898391 12.5794392 255.4967487 0.0000000 18 1.9865 19 2.1519 18 1.9586 19 2.2042 +A_92_P024516 1 3 1 23 2.7904 11.7412564 2.5478526388 0.1205252 0.3260419 11.5022960 -218.6650149 0.0000000 21 2.6455 23 2.9188 21 2.6407 23 2.9708 +A_92_P023713 2 1 2 1 0.1001 15.0930867 3.2751998139 0.1490762 0.3233012 1.0763490 252.8027941 0.0000000 1 0.0085 2 0.2729 1 0.0001 2 0.3274 +A_92_P023713 2 3 5 16 1.6832 20.6465042 4.4802914114 0.2378846 0.3902667 0.2904053 323.5459459 0.0000000 15 1.6398 16 1.7329 15 1.6326 16 1.7647 +A_92_P023713 2 5 6 3 0.2255 13.1162156 2.8462187852 0.1138979 0.3974125 3.4227484 -218.8805035 0.0000000 1 0.0163 4 0.3178 1 0.0001 4 0.3477 +A_92_P023551 3 1 1 14 1.6098 12.1963674 2.6466117258 0.1372960 0.3800574 4.6993484 133.4043424 0.0000000 14 1.5338 15 1.6972 13 1.4897 15 1.7507 +A_92_P023551 3 2 10 1 0.0601 19.0928858 4.1431562186 0.2468352 0.4758394 0.5013347 175.2143455 0.0000000 1 0.0045 1 0.1223 1 0.0001 1 0.1422 |
| b |
| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/output/qtl_out_13.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/output/qtl_out_13.txt Fri Mar 18 05:51:39 2016 -0400 |
| b |
| @@ -0,0 +1,4 @@ +A_92_P023080 3 1 1 1 0.0601 37.7011957 8.1811594669 0.2848013 0.9322797 1.6358983 104.0142532 0.0000000 1 0.0317 2 0.1189 1 0.0187 2 0.1296 +A_92_P023080 3 3 1 20 2.3609 13.6788863 2.9683183271 0.0553721 0.8882827 3.8493444 -32.3646289 0.0000000 19 2.2733 20 2.4304 19 2.2101 20 2.4852 +A_92_P023080 3 4 7 11 1.1032 31.0287041 6.7332287897 0.1789058 0.8966296 3.4735566 -67.0784555 0.0000000 10 1.0607 11 1.1032 10 1.0104 11 1.1032 +A_92_P023080 3 5 8 5 0.5015 51.6576621 11.2097126757 0.4555327 0.8732000 3.3751192 -96.9461713 0.0000000 4 0.4549 5 0.5372 4 0.4234 5 0.5707 |
| b |
| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/output/qtl_out_14.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/output/qtl_out_14.txt Fri Mar 18 05:51:39 2016 -0400 |
| b |
| @@ -0,0 +1,7 @@ +A_92_P022918 1 1 8 1 0.0401 31.7555607 6.8909566719 0.3030513 0.5086103 5.0865774 -681.3026366 0.0000000 1 0.0111 1 0.0817 1 0.0001 1 0.0967 +A_92_P022755 2 1 3 16 1.9454 12.2519892 2.6586816564 0.1092460 0.4087476 8.3542742 -1752.0761466 0.0000000 15 1.8842 17 2.1202 15 1.8784 17 2.1344 +A_92_P022755 2 4 8 4 0.4274 20.6933638 4.4904599446 0.1369886 0.5115352 6.5683702 1984.0754662 0.0000000 3 0.2923 5 0.5831 3 0.264 5 0.6403 +A_92_P022755 2 6 9 7 0.9782 16.3122115 3.5397498955 0.1202802 0.3841991 7.0636630 -1823.7633241 0.0000000 6 0.9287 7 1.0488 5 0.8089 7 1.0942 +A_92_P022755 2 7 10 11 1.1764 13.8857650 3.013211005 0.1003230 0.3792059 7.0186621 -1705.3060098 0.0000000 10 1.1196 11 1.225 10 1.0773 11 1.2614 +A_92_P022592 3 1 1 13 1.4670 14.1819258 3.0774778986 0.1495470 0.3618150 9.7749401 -73.0555529 0.0000000 13 1.4278 14 1.5786 12 1.4169 14 1.6308 +A_92_P022592 3 2 1 18 2.0143 11.8257352 2.5661845384 0.1011971 0.3249504 7.5422339 52.5612035 0.0000000 18 1.9421 19 2.1435 17 1.8757 19 2.2445 |
| b |
| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/output/qtl_out_15.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/output/qtl_out_15.txt Fri Mar 18 05:51:39 2016 -0400 |
| b |
| @@ -0,0 +1,7 @@ +A_92_P022110 1 1 1 18 2.0143 12.0455951 2.6138941367 0.0928423 0.3268055 0.5377619 140.2867239 0.0000000 17 1.9036 19 2.1396 16 1.8722 19 2.2243 +A_92_P022110 1 2 10 12 1.4054 13.2804218 2.8818515306 0.1419048 0.3733549 0.3170982 -169.0318841 0.0000000 12 1.3123 12 1.4654 11 1.2993 12 1.4654 +A_92_P021792 2 1 1 14 1.6098 13.7867804 2.9917313468 0.1154861 0.4159935 1.5415854 -187.9840206 0.0000000 14 1.526 15 1.7162 13 1.4892 15 1.7577 +A_92_P021792 2 2 1 19 2.0214 21.2959774 4.6212270958 0.1459124 0.3894262 1.6071086 212.4539382 0.0000000 18 1.973 19 2.1178 18 1.9474 19 2.1703 +A_92_P021792 2 3 7 3 0.2061 14.4512266 3.1359161722 0.0953207 0.3877693 1.6159454 -166.6958319 0.0000000 2 0.1497 3 0.2588 2 0.1091 3 0.2887 +A_92_P021792 2 4 10 10 1.0861 19.1017279 4.1450749543 0.1666632 0.4539051 0.0927683 -215.6184203 0.0000000 9 1.0403 10 1.1595 9 1.0153 10 1.1695 +A_92_P021634 3 1 6 16 1.9423 30.9698873 6.7204655441 0.2910527 0.3081694 2.0286370 795.9301198 0.0000000 16 1.9009 16 1.9423 16 1.8746 16 1.9423 |
| b |
| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/output/qtl_out_2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/output/qtl_out_2.txt Fri Mar 18 05:51:39 2016 -0400 |
| b |
| @@ -0,0 +1,12 @@ +A_92_P037834 1 1 4 5 0.5309 24.0416490 5.217037833 0.1788150 0.4904768 20.2186322 -215.1013986 0.0000000 4 0.483 5 0.5471 4 0.4502 5 0.5558 +A_92_P037834 1 2 5 19 1.9955 12.8100275 2.7797759675 0.1007023 0.5007851 24.0032764 -164.1721772 0.0000000 18 1.9338 19 2.0355 16 1.7878 19 2.0355 +A_92_P037834 1 3 7 3 0.2861 28.3465676 6.1512051692 0.2712756 0.5525036 11.0181706 274.5318342 0.0000000 3 0.2457 4 0.3541 3 0.2299 4 0.382 +A_92_P037509 2 1 2 5 0.8205 20.9015193 4.5356296881 0.1920072 0.8228764 0.6300379 50.7070865 0.0000000 4 0.7702 5 0.8741 4 0.7317 5 0.8958 +A_92_P037509 2 2 3 14 1.7522 14.5634804 3.1602752468 0.1395012 0.8505212 0.6992039 43.6613918 0.0000000 14 1.6705 15 1.84 14 1.6376 15 1.8775 +A_92_P037509 2 3 6 15 1.7431 18.4634837 4.0065759629 0.1907638 0.8576937 0.9327344 52.4041957 0.0000000 15 1.6376 16 1.9224 14 1.6228 16 1.9367 +A_92_P037509 2 5 8 5 0.5015 28.4825171 6.1807062107 0.3078012 0.8259992 0.6597413 -63.9160300 0.0000000 4 0.4414 5 0.5539 4 0.419 5 0.5893 +A_92_P037035 3 1 2 8 1.1375 32.8400994 7.1263015698 0.2303759 0.5341618 178.1779135 -434.9303913 0.0000000 7 1.0942 8 1.1598 7 1.0586 8 1.1634 +A_92_P037035 3 2 2 10 1.3263 16.5244802 3.5858122034 0.0980168 0.5049068 100.6701175 284.2624983 0.0000000 9 1.322 10 1.3666 9 1.3177 10 1.4038 +A_92_P037035 3 3 9 7 0.9782 39.2967801 8.5274012817 0.2607592 0.5063220 118.6289643 -382.9703278 0.0000000 6 0.9547 7 1.0159 6 0.9389 7 1.046 +A_92_P036877 4 1 2 7 1.0104 13.6743073 2.9673246841 0.1091632 0.3352177 193.4943050 151.5554180 0.0000000 6 0.934 7 1.0843 5 0.9044 7 1.113 +A_92_P036877 4 2 4 11 1.1329 15.8680278 3.4433620326 0.1814249 0.3996043 198.2704407 -204.6505552 0.0000000 11 1.1138 11 1.1821 10 1.1081 13 1.3664 |
| b |
| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/output/qtl_out_3.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/output/qtl_out_3.txt Fri Mar 18 05:51:39 2016 -0400 |
| b |
| @@ -0,0 +1,10 @@ +A_92_P036723 1 1 3 2 0.1176 25.5451801 5.5433040817 0.3367142 0.7495437 0.1420987 30.1380150 0.0000000 1 0.0634 2 0.1606 1 0.0373 2 0.193 +A_92_P036723 1 2 3 5 0.5925 12.4777349 2.7076684733 0.1140458 0.8663131 0.6745923 19.2755898 0.0000000 5 0.5496 5 0.6126 5 0.5279 5 0.6129 +A_92_P036723 1 4 3 18 2.1961 20.6998468 4.4918667556 0.2566942 0.7530538 0.1563160 27.1528712 0.0000000 18 2.1488 18 2.1961 17 2.0507 18 2.1961 +A_92_P036723 1 5 6 14 1.5977 11.7592146 2.5517495682 0.1189907 0.7522249 0.1368680 -18.8320617 0.0000000 13 1.4591 15 1.6792 12 1.3915 15 1.8129 +A_92_P036564 2 1 1 17 1.9125 14.0649598 3.0520962766 0.1257104 0.3385352 8.3880503 178.1987126 0.0000000 16 1.8419 18 2.0148 16 1.8028 18 2.0189 +A_92_P036564 2 3 4 12 1.2426 11.7618881 2.5523297177 0.1027206 0.3215265 9.5874467 -163.3414051 0.0000000 11 1.1355 13 1.361 10 1.0381 13 1.3718 +A_92_P036402 3 1 3 3 0.3960 11.9578142 2.5948456814 0.1717407 0.6684378 37.0007748 33.8745914 0.0000000 2 0.2539 5 0.5279 2 0.2406 5 0.6001 +A_92_P036402 3 2 10 12 1.4654 13.2511287 2.8754949279 0.1735358 0.6527381 31.4598473 31.5911238 0.0000000 12 1.3866 12 1.4654 12 1.327 12 1.4654 +A_92_P036241 4 1 5 17 1.7894 12.4339606 2.6981694502 0.0944238 0.3150629 15.8341283 -207.6782322 0.0000000 16 1.733 17 1.8612 16 1.6728 17 1.8975 +A_92_P036241 4 2 10 1 0.0401 11.8407342 2.5694393214 0.1081500 0.3340395 19.0765856 221.2449803 0.0000000 1 0.0001 1 0.1413 1 0.0001 1 0.1475 |
| b |
| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/output/qtl_out_4.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/output/qtl_out_4.txt Fri Mar 18 05:51:39 2016 -0400 |
| b |
| @@ -0,0 +1,6 @@ +A_92_P036076 1 1 6 1 0.0201 12.0508049 2.6150246633 0.0638608 0.7313758 5.7647286 -148.2950721 0.0000000 1 0.0001 3 0.2309 1 0.0001 3 0.288 +A_92_P036076 1 2 8 4 0.3874 63.8836181 13.8627451277 0.5007644 0.7018512 12.7850245 -411.4754368 0.0000000 3 0.3594 4 0.4126 3 0.3341 4 0.4342 +A_92_P035602 2 1 3 7 0.7403 33.6744317 7.3073516789 0.3067255 0.5170118 11.8654223 -88.4458067 0.0000000 6 0.7166 7 0.7641 6 0.6808 7 0.7728 +A_92_P035118 3 1 2 6 0.9061 11.9240992 2.5875295264 0.1226207 0.4624417 11.3460016 -51.7009439 0.0000000 5 0.854 6 0.9836 3 0.6382 6 1.0072 +A_92_P035118 3 2 2 10 1.4063 20.1741062 4.3777810454 0.2324464 0.5069494 0.0863209 84.9271020 0.0000000 10 1.3551 11 1.4363 10 1.3341 11 1.492 +A_92_P035118 3 4 10 8 0.9063 13.5647584 2.9435525728 0.1296273 0.4429836 11.9072611 58.1585016 0.0000000 7 0.8506 8 0.9832 5 0.7509 9 1.0316 |
| b |
| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/output/qtl_out_5.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/output/qtl_out_5.txt Fri Mar 18 05:51:39 2016 -0400 |
| b |
| @@ -0,0 +1,6 @@ +A_92_P034794 1 2 10 2 0.1903 13.7851819 2.9913844723 0.1500800 0.4826392 1.3172075 37.9229818 0.0000000 1 0.0205 2 0.2714 1 0.0001 2 0.3136 +A_92_P034308 2 1 1 10 1.0811 21.5408069 4.6743550973 0.2277382 0.7592832 1.5834036 -33.7902103 0.0000000 10 0.994 11 1.2061 10 0.9663 11 1.2428 +A_92_P034308 2 2 3 18 2.1361 37.6966811 8.1801797987 0.4294746 0.7461673 0.5001206 -46.4689965 0.0000000 17 2.0979 18 2.1767 17 2.0704 18 2.1961 +A_92_P034308 2 4 6 15 1.6231 15.0777058 3.2718621586 0.1278544 0.7208327 0.6238438 -25.3129593 0.0000000 14 1.6037 15 1.7696 12 1.3838 15 1.8092 +A_92_P033825 3 1 5 12 1.2112 26.3566078 5.7193838926 0.2959435 0.6404193 5.3064385 75.0605964 0.0000000 12 1.1492 13 1.2967 12 1.124 13 1.3275 +A_92_P033667 4 1 1 10 1.0011 32.5164489 7.0560694113 0.2841753 0.6066141 14.4318293 -402.5391792 0.0000000 9 0.9597 10 1.0702 9 0.9144 10 1.1011 |
| b |
| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/output/qtl_out_6.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/output/qtl_out_6.txt Fri Mar 18 05:51:39 2016 -0400 |
| b |
| @@ -0,0 +1,11 @@ +A_92_P033184 1 1 2 6 0.9061 14.8587743 3.2243540231 0.2333258 0.6091560 22.0542994 -38.6663227 0.0000000 5 0.8719 6 0.9577 5 0.8433 6 0.9883 +A_92_P033019 2 1 4 1 0.0001 18.0264218 3.9117335306 0.2358947 0.7043399 1.1338535 -36.1921190 0.0000000 1 0.0001 1 0.1049 1 0.0001 1 0.1658 +A_92_P033019 2 3 4 14 1.3767 24.4933746 5.3150622882 0.3512706 0.6952266 0.7481420 -44.9542340 0.0000000 13 1.3132 14 1.4571 13 1.291 14 1.4719 +A_92_P033019 2 4 8 9 1.0132 12.4174801 2.6945931817 0.1576451 0.7132070 1.5293308 -31.2505707 0.0000000 8 0.9674 10 1.0946 6 0.8291 10 1.1515 +A_92_P032694 3 1 7 8 0.6320 32.1699934 6.9808885678 0.2420005 0.6003624 24.9291265 344.4116975 0.0000000 7 0.5956 8 0.6784 7 0.5757 8 0.7048 +A_92_P032694 3 2 7 10 0.8764 13.4413200 2.91676644 0.0878881 0.5980498 25.7814583 206.5255165 0.0000000 9 0.7973 10 1.0197 5 0.4516 10 1.0602 +A_92_P032375 4 1 5 16 1.7032 16.9984527 3.6886642359 0.1302289 0.5128756 27.8335593 107.9491425 0.0000000 15 1.5695 16 1.7838 15 1.5206 16 1.7866 +A_92_P032375 4 2 7 7 0.5545 25.7188796 5.5809968732 0.1610310 0.4683558 29.9770539 119.3799447 0.0000000 6 0.5181 7 0.583 6 0.4944 7 0.6026 +A_92_P032375 4 3 8 1 0.1001 19.6244369 4.2585028073 0.1304073 0.4749124 32.9505567 -126.1800898 0.0000000 1 0.0263 2 0.1759 1 0.0001 2 0.2199 +A_92_P032375 4 4 8 5 0.5015 12.1700046 2.6408909982 0.0729679 0.4682935 31.2541491 94.9172785 0.0000000 4 0.4357 5 0.5812 4 0.4057 5 0.6382 +A_92_P032375 4 5 9 8 1.2252 11.9054995 2.5834933915 0.0724122 0.4722985 30.5643015 83.1749874 0.0000000 7 1.1385 9 1.3136 7 1.083 9 1.3852 |
| b |
| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/output/qtl_out_7.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/output/qtl_out_7.txt Fri Mar 18 05:51:39 2016 -0400 |
| b |
| @@ -0,0 +1,3 @@ +A_92_P031891 1 1 3 6 0.7129 12.1291440 2.632024248 0.1463481 0.4572059 3.3024336 22.7464054 0.0000000 6 0.6425 7 0.7575 5 0.6128 9 0.8513 +A_92_P031571 2 1 1 9 0.8188 15.5773107 3.3802764219 0.1576819 0.6595742 4.9462336 30.4289126 0.0000000 8 0.7654 9 0.9028 8 0.7266 9 0.9461 +A_92_P030934 4 1 1 12 1.3484 12.7269818 2.7617550506 0.1554477 0.3181084 11.0051898 1307.8971923 0.0000000 11 1.2068 12 1.4126 10 1.1262 12 1.4225 |
| b |
| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/output/qtl_out_8.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/output/qtl_out_8.txt Fri Mar 18 05:51:39 2016 -0400 |
| b |
| @@ -0,0 +1,5 @@ +A_92_P030772 1 1 1 12 1.2884 14.6017579 3.1685814643 0.1322083 0.3547828 68.3702870 92.1827784 0.0000000 11 1.1967 12 1.3849 11 1.1334 12 1.4137 +A_92_P030772 1 2 2 8 1.1175 12.2942458 2.6678513386 0.0951207 0.3365067 55.8325996 91.5133766 0.0000000 7 1.0195 8 1.1608 6 1.0079 8 1.1701 +A_92_P029488 3 1 1 23 2.7504 12.7423639 2.7650929663 0.0886911 0.3771941 0.6115715 -170.6386723 0.0000000 22 2.6575 23 2.8791 21 2.6432 23 2.9422 +A_92_P029488 3 2 4 14 1.4567 15.7422210 3.416061957 0.1252436 0.3938654 0.8032518 -197.3601638 0.0000000 14 1.3938 15 1.5144 13 1.342 16 1.6101 +A_92_P029164 4 2 2 12 1.5405 22.4499094 4.8716303398 0.3269444 0.5618480 132.0731880 -1222.1310894 0.0000000 11 1.4693 12 1.6362 11 1.4302 12 1.6609 |
| b |
| diff -r 000000000000 -r fa0693cf076b qtlmap_15/test-data/output/qtl_out_9.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qtlmap_15/test-data/output/qtl_out_9.txt Fri Mar 18 05:51:39 2016 -0400 |
| b |
| @@ -0,0 +1,5 @@ +A_92_P028842 2 1 2 7 1.0904 28.2461323 6.1294107091 0.3118840 0.5439671 5.6068692 -54.5035913 0.0000000 7 1.0324 8 1.1416 7 1.0179 8 1.1585 +A_92_P028842 2 2 3 12 1.3680 18.5426079 4.0237459143 0.1741882 0.5155299 3.8667059 -33.5409799 0.0000000 11 1.3328 12 1.4349 11 1.3142 12 1.4792 +A_92_P028042 4 1 1 11 1.2671 38.7087949 8.3998084933 0.3305027 0.4144519 2.1621607 120.1256345 0.0000000 11 1.2357 11 1.2675 11 1.2082 11 1.2679 +A_92_P028042 4 2 1 14 1.4898 13.3623833 2.8996371761 0.1034618 0.3996348 4.3479198 -71.0505158 0.0000000 13 1.4431 14 1.547 10 1.123 14 1.5891 +A_92_P028042 4 4 9 10 1.4239 17.8301407 3.8691405319 0.1743896 0.4645963 0.1983911 73.9224765 0.0000000 9 1.3211 10 1.4971 9 1.2873 10 1.5309 |