bio-polyploid-tools 0.7.3 → 0.8.0

data/test/data/S58861868/S58861868.fa

@@ -0,0 +1,16 @@
+>gnl|UG|Ta#S58861868
+CTTTGAAAATGAGCGCTTGCAATCCTTGAAGTTGCATTTAATCCTCTCAGTGACAAACGA
+ACCTTCATGCATTCGCTGATGCCGCTTGAAGTTCTTCTTAAGCTGTTTAGTGTCACAGAT
+ATCACACTGAACATACTGATGACACGATTGGTTATGGGCCTTGAGGCATTCCACATTAGT
+AAAAGTCTTCATGCAGCCTGGTTCGCAGCAGATAACTTCAGTGTAATCCAAGTTGACATG
+TGATTCCTCGTGTTTCTGTAGCTTGGAAGCATATTTGAACACCTTCCCACAGTTAGCCTC
+TGGGCAGATGAACTCTTTCTTGCCTCCACACTGAGGGCCATCCTCGTGAAATTCCTCAAC
+ATGTCTCTGGATATTACCCTTGATACTGAACTTACGGTTGCATCCTTCCATAGGGCACAT
+GAATAGTTTTCCGTGATGAGTAAGCAGATGGCGGTTCAAATGGTCCTTCCTGCTATAGCT
+GAAAGGGCAACCATCTACATGGCAGGCAAAGGGTCTCTGAGGAAGCGCGTGAATGAGGCA
+TTCTTGATGGAGCTTCTCAGGAGGGTCTCCCCTTCCTGATACTGGTCCATTCAAGGCCTT
+CTGGCATTTTGGAGTTCTTGGGATCCAATGCTTCACACATTCATATCTGAACATGTAGTC
+TGAAGAAGGGCGTGAAAGAGGCTTCCTGAAGGAGCTTCCCAGGAGGGTCTCCCCATCCTG
+GTACTAGTCCATTCAGGGCCCTCTCGCATTTTGGAGTTCTTTGGGATCCAATGCTTCACA
+CAATTAAATAGCCTCAAGCGAATGGCTCTGCATATGCTGCTTCAGATGCGCCGGCTTCTT
+AAA

data/test/data/S58861868/S58861868.fa.fai

@@ -0,0 +1 @@
+gnl|UG|Ta#S58861868	843	21	60	61

data/test/data/S58861868/S58861868.vcf

@@ -0,0 +1,76 @@
+##fileformat=VCFv4.1
+##fileDate=20160614
+##source=freeBayes v1.0.2-dirty
+##reference=S58861868.fa
+##phasing=none
+##commandline="freebayes -f S58861868.fa merged_reheader.bam"
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
+##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
+##INFO=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally">
+##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">
+##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">
+##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">
+##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
+##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
+##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations">
+##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations">
+##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">
+##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">
+##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand">
+##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand">
+##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
+##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">
+##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele">
+##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele">
+##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio.  Ratio between depth in samples with each called alternate allele and those without.">
+##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best.">
+##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout.">
+##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
+##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing.  Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.">
+##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position.">
+##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.">
+##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
+##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles">
+##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles">
+##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments">
+##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments">
+##INFO=<ID=MIN,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
+##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record.">
+##INFO=<ID=technology.Illumina,Number=A,Type=Float,Description="Fraction of observations supporting the alternate observed in reads from Illumina">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
+##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
+##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
+##FORMAT=<ID=MIN,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	AVS	Yr15	R2	S2
+gnl|UG|Ta#S58861868	37	.	T	C	1258.55	.	AB=0.398693;ABP=16.6494;AC=4;AF=0.5;AN=8;AO=61;CIGAR=1X;DP=153;DPB=153;DPRA=0;EPP=5.89373;EPPR=9.05266;GTI=0;LEN=1;MEANALT=1;MQM=50.1967;MQMR=46.25;NS=4;NUMALT=1;ODDS=54.792;PAIRED=0.57377;PAIREDR=0.402174;PAO=0;PQA=0;PQR=0;PRO=0;QA=2270;QR=3315;RO=92;RPL=0;RPP=135.47;RPPR=202.786;RPR=61;RUN=1;SAF=35;SAP=5.89373;SAR=26;SRF=38;SRP=9.05266;SRR=54;TYPE=snp;technology.Illumina=1	GT:DP:RO:QR:AO:QA:GL	0/1:56:38:1354:18:683:-43.4491,0,-100.617	0/1:35:16:579:19:716:-52.4805,0,-40.6735	0/1:29:17:621:12:432:-29.5593,0,-45.5261	0/1:33:21:761:12:439:-28.6261,0,-56.6031
+gnl|UG|Ta#S58861868	58	.	C	T	2562.59	.	AB=0.428571;ABP=14.4881;AC=4;AF=0.5;AN=8;AO=111;CIGAR=1X;DP=259;DPB=259;DPRA=0;EPP=10.0725;EPPR=5.12308;GTI=0;LEN=1;MEANALT=1;MQM=50.6757;MQMR=47.4122;NS=4;NUMALT=1;ODDS=105.177;PAIRED=0.594595;PAIREDR=0.452703;PAO=0;PQA=0;PQR=0;PRO=0;QA=4155;QR=5450;RO=148;RPL=11;RPP=157.967;RPPR=200.438;RPR=100;RUN=1;SAF=62;SAP=6.31642;SAR=49;SRF=62;SRP=11.4614;SRR=86;TYPE=snp;technology.Illumina=1	GT:DP:RO:QR:AO:QA:GL	0/1:85:52:1936:33:1248:-83.822,0,-140.119	0/1:65:28:1036:37:1404:-102.65,0,-70.9658	0/1:51:31:1122:20:743:-49.6245,0,-81.6444	0/1:58:37:1356:21:760:-49.4165,0,-99.6141
+gnl|UG|Ta#S58861868	143	.	C	G	3221.35	.	AB=0.333333;ABP=107.241;AC=4;AF=0.5;AN=8;AO=144;CIGAR=1X;DP=432;DPB=432;DPRA=0;EPP=3.25157;EPPR=7.01277;GTI=0;LEN=1;MEANALT=1.25;MQM=52.8125;MQMR=53.9094;NS=4;NUMALT=1;ODDS=121.053;PAIRED=0.6875;PAIREDR=0.731707;PAO=0;PQA=0;PQR=0;PRO=0;QA=5440;QR=10703;RO=287;RPL=90;RPP=22.5536;RPPR=24.2635;RPR=54;RUN=1;SAF=58;SAP=14.8328;SAR=86;SRF=138;SRP=3.9258;SRR=149;TYPE=snp;technology.Illumina=1	GT:DP:RO:QR:AO:QA:GL	0/1:143:94:3546:49:1854:-118.654,0,-268.576	0/1:122:93:3424:29:1121:-60.9339,0,-265.65	0/1:79:46:1747:32:1176:-79.1788,0,-130.071	0/1:88:54:1986:34:1289:-86.7471,0,-146.355
+gnl|UG|Ta#S58861868	165	.	G	A	4173.04	.	AB=0.391705;ABP=47.2203;AC=4;AF=0.5;AN=8;AO=170;CIGAR=1X;DP=434;DPB=434;DPRA=0;EPP=6.28028;EPPR=11.433;GTI=0;LEN=1;MEANALT=1;MQM=55.8059;MQMR=55.8182;NS=4;NUMALT=1;ODDS=143.249;PAIRED=0.811765;PAIREDR=0.818182;PAO=0;PQA=0;PQR=0;PRO=0;QA=6363;QR=9918;RO=264;RPL=93;RPP=6.28028;RPPR=3.1419;RPR=77;RUN=1;SAF=84;SAP=3.06139;SAR=86;SRF=132;SRP=3.0103;SRR=132;TYPE=snp;technology.Illumina=1	GT:DP:RO:QR:AO:QA:GL	0/1:146:85:3206:61:2294:-157.55,0,-239.796	0/1:121:68:2515:53:1967:-138.716,0,-185.289	0/1:80:53:1990:27:1010:-66.4621,0,-151.983	0/1:87:58:2207:29:1092:-69.5239,0,-168.981
+gnl|UG|Ta#S58861868	206	.	C	A	3480.93	.	AB=0.358586;ABP=71.7955;AC=4;AF=0.5;AN=8;AO=142;CIGAR=1X;DP=396;DPB=396;DPRA=0;EPP=6.92507;EPPR=4.26107;GTI=0;LEN=1;MEANALT=1.5;MQM=57.0845;MQMR=58.528;NS=4;NUMALT=1;ODDS=109.904;PAIRED=0.866197;PAIREDR=0.936;PAO=0;PQA=0;PQR=0;PRO=0;QA=5429;QR=9481;RO=250;RPL=75;RPP=3.98899;RPPR=3.5662;RPR=67;RUN=1;SAF=60;SAP=10.4117;SAR=82;SRF=130;SRP=3.87889;SRR=120;TYPE=snp;technology.Illumina=1	GT:DP:RO:QR:AO:QA:GL	0/1:132:80:3009:52:1983:-136.758,0,-229.913	0/1:108:63:2397:45:1721:-120.275,0,-181.592	0/1:70:47:1798:22:843:-54.9106,0,-139.692	0/1:86:60:2277:23:882:-53.6092,0,-178.381
+gnl|UG|Ta#S58861868	214	.	A	G	978.837	.	AB=0.281768;ABP=77.8841;AC=2;AF=0.25;AN=8;AO=52;CIGAR=1X;DP=406;DPB=406;DPRA=0.661765;EPP=5.68288;EPPR=5.97921;GTI=0;LEN=1;MEANALT=1;MQM=56.9038;MQMR=58.2458;NS=4;NUMALT=1;ODDS=76.6372;PAIRED=0.865385;PAIREDR=0.923729;PAO=0;PQA=0;PQR=0;PRO=0;QA=1939;QR=13255;RO=354;RPL=23;RPP=4.51363;RPPR=3.89361;RPR=29;RUN=1;SAF=23;SAP=4.51363;SAR=29;SRF=177;SRP=3.0103;SRR=177;TYPE=snp;technology.Illumina=1	GT:DP:RO:QR:AO:QA:GL	0/0:136:136:4997:0:0:0,-40.9401,-447.231	0/1:113:81:3081:32:1203:-73.029,0,-240.801	0/1:68:49:1877:19:695:-41.7608,0,-148.168	0/0:89:88:3300:1:41:0,-22.6971,-291.665
+gnl|UG|Ta#S58861868	281	.	A	G	8179.22	.	AB=0.699531;ABP=150.324;AC=4;AF=0.5;AN=8;AO=298;CIGAR=1X;DP=426;DPB=426;DPRA=0;EPP=11.4339;EPPR=6.33537;GTI=0;LEN=1;MEANALT=1;MQM=58.5336;MQMR=59.2812;NS=4;NUMALT=1;ODDS=35.8044;PAIRED=0.936242;PAIREDR=0.96875;PAO=0;PQA=0;PQR=0;PRO=0;QA=10858;QR=4262;RO=128;RPL=151;RPP=3.12689;RPPR=3.07816;RPR=147;RUN=1;SAF=135;SAP=8.72317;SAR=163;SRF=54;SRP=9.79615;SRR=74;TYPE=snp;technology.Illumina=1	GT:DP:RO:QR:AO:QA:GL	0/1:145:53:1775:92:3405:-261.359,0,-116.331	0/1:122:37:1228:85:3166:-247.062,0,-74.0174	0/1:63:15:501:48:1726:-135.971,0,-26.4254	0/1:96:23:758:73:2561:-200.272,0,-39.3854
+gnl|UG|Ta#S58861868	330	.	A	G	4061.09	.	AB=0.391608;ABP=46.789;AC=4;AF=0.5;AN=8;AO=168;CIGAR=1X;DP=429;DPB=429;DPRA=0;EPP=3.0103;EPPR=6.67934;GTI=0;LEN=1;MEANALT=1;MQM=59.0417;MQMR=58.8544;NS=4;NUMALT=1;ODDS=165.83;PAIRED=0.958333;PAIREDR=0.950192;PAO=0;PQA=0;PQR=0;PRO=0;QA=6121;QR=9667;RO=261;RPL=79;RPP=4.30284;RPPR=5.41473;RPR=89;RUN=1;SAF=85;SAP=3.062;SAR=83;SRF=120;SRP=6.67934;SRR=141;TYPE=snp;technology.Illumina=1	GT:DP:RO:QR:AO:QA:GL	0/1:141:85:3100:56:2110:-146.694,0,-235.683	0/1:118:84:3125:34:1234:-75.8243,0,-244.64	0/1:79:44:1678:35:1226:-86.821,0,-127.129	0/1:91:48:1764:43:1551:-111.142,0,-131.124
+gnl|UG|Ta#S58861868	331	.	CT	AT,AC	2730.19	.	AB=0.318339,0.189103;ABP=85.8493,264.951;AC=3,1;AF=0.375,0.125;AN=8;AO=92,59;CIGAR=1X1M,2X;DP=430;DPB=434.5;DPRA=0,0;EPP=5.3706,3.34154;EPPR=6.13472;GTI=0;LEN=1,2;MEANALT=2,2;MQM=59.5,59.6102;MQMR=58.5108;NS=4;NUMALT=2;ODDS=62.584;PAIRED=0.978261,0.983051;PAIREDR=0.935252;PAO=2.5,1;PQA=0,30;PQR=91;PRO=5.5;QA=3419,2130;QR=10273;RO=278;RPL=49,23;RPP=3.86001,9.23028;RPPR=3.04154;RPR=43,36;RUN=1,1;SAF=40,30;SAP=6.40913,3.0471;SAR=52,29;SRF=137;SRP=3.13528;SRR=141;TYPE=snp,mnp;technology.Illumina=1,1	GT:DP:RO:QR:AO:QA:GL	0/2:141:103:3865:0,38:0,1355:-78.1426,-110.654,-426.731,0,-317.641,-303.794	0/1:118:66:2444:52,0:1939,0:-137.893,0,-184.569,-156.267,-198.427,-355.518	0/1:80:50:1815:20,9:743,336:-45.1572,0,-140.859,-33.3033,-119.976,-176.863	0/1:91:59:2149:20,12:737,439:-41.3704,0,-170.405,-24.1641,-141.156,-196.374
+gnl|UG|Ta#S58861868	433	.	G	T	9002.83	.	AB=0.718468;ABP=187.077;AC=4;AF=0.5;AN=8;AO=319;CIGAR=1X;DP=444;DPB=444;DPRA=0;EPP=3.34385;EPPR=13.8677;GTI=0;LEN=1;MEANALT=1;MQM=57.4357;MQMR=57.792;NS=4;NUMALT=1;ODDS=78.8301;PAIRED=0.893417;PAIREDR=0.904;PAO=0;PQA=0;PQR=0;PRO=0;QA=11963;QR=4618;RO=125;RPL=151;RPP=4.97756;RPPR=3.44459;RPR=168;RUN=1;SAF=165;SAP=3.83396;SAR=154;SRF=66;SRP=3.86152;SRR=59;TYPE=snp;technology.Illumina=1	GT:DP:RO:QR:AO:QA:GL	0/1:150:40:1479:110:4154:-326.794,0,-86.822	0/1:126:39:1436:87:3248:-246.869,0,-89.259	0/1:78:21:777:57:2166:-170.27,0,-46.2794	0/1:90:25:926:65:2395:-185.917,0,-56.2843
+gnl|UG|Ta#S58861868	445	.	C	T	3908.73	.	AB=0.378995;ABP=58.715;AC=4;AF=0.5;AN=8;AO=166;CIGAR=1X;DP=438;DPB=438;DPRA=0;EPP=9.34158;EPPR=16.4798;GTI=0;LEN=1;MEANALT=1.25;MQM=57.6386;MQMR=57.4945;NS=4;NUMALT=1;ODDS=152.434;PAIRED=0.903614;PAIREDR=0.892989;PAO=0;PQA=0;PQR=0;PRO=0;QA=6050;QR=10067;RO=271;RPL=81;RPP=3.2196;RPPR=3.01831;RPR=85;RUN=1;SAF=79;SAP=3.84749;SAR=87;SRF=150;SRP=9.74908;SRR=121;TYPE=snp;technology.Illumina=1	GT:DP:RO:QR:AO:QA:GL	0/1:149:95:3576:54:1989:-133.144,0,-274.817	0/1:123:84:3145:39:1437:-88.3527,0,-241.679	0/1:79:37:1334:42:1538:-114.631,0,-95.3496	0/1:87:55:2012:31:1086:-70.8322,0,-153.545
+gnl|UG|Ta#S58861868	486	.	G	T	1357.23	.	AB=0.328205;ABP=52.9987;AC=2;AF=0.25;AN=8;AO=67;CIGAR=1X;DP=407;DPB=407;DPRA=0.671605;EPP=3.04271;EPPR=4.26209;GTI=0;LEN=1;MEANALT=1;MQM=58.6269;MQMR=57.5647;NS=4;NUMALT=1;ODDS=72.5294;PAIRED=0.940299;PAIREDR=0.894118;PAO=0;PQA=0;PQR=0;PRO=0;QA=2392;QR=12450;RO=340;RPL=42;RPP=12.3768;RPPR=14.2764;RPR=25;RUN=1;SAF=33;SAP=3.04271;SAR=34;SRF=158;SRP=6.68903;SRR=182;TYPE=snp;technology.Illumina=1	GT:DP:RO:QR:AO:QA:GL	0/0:135:135:4949:0:0:0,-40.639,-440.374	0/1:118:82:3035:36:1306:-81.6818,0,-234.6	0/1:77:49:1831:28:1007:-67.5957,0,-140.738	0/0:77:74:2635:3:79:0,-15.8074,-227.645
+gnl|UG|Ta#S58861868	641	.	T	C	2230.32	.	AB=0.373494;ABP=37.623;AC=4;AF=0.5;AN=8;AO=93;CIGAR=1X;DP=249;DPB=249;DPRA=0;EPP=15.362;EPPR=14.7923;GTI=0;LEN=1;MEANALT=1.25;MQM=57.2796;MQMR=55.8452;NS=4;NUMALT=1;ODDS=88.7991;PAIRED=0.88172;PAIREDR=0.819355;PAO=0;PQA=0;PQR=0;PRO=0;QA=3503;QR=5857;RO=155;RPL=44;RPP=3.59403;RPPR=6.16244;RPR=49;RUN=1;SAF=36;SAP=13.3073;SAR=57;SRF=72;SRP=4.70545;SRR=83;TYPE=snp;technology.Illumina=1	GT:DP:RO:QR:AO:QA:GL	0/1:107:69:2613:37:1432:-94.9944,0,-197.948	0/1:58:36:1378:22:796:-53.917,0,-105.047	0/1:35:18:680:17:650:-47.3435,0,-50.4266	0/1:49:32:1186:17:625:-41.8177,0,-90.9036
+gnl|UG|Ta#S58861868	780	.	A	G	460.928	.	AB=0.260504;ABP=62.297;AC=4;AF=0.5;AN=8;AO=31;CIGAR=1X;DP=119;DPB=119;DPRA=0;EPP=4.76149;EPPR=59.8634;GTI=0;LEN=1;MEANALT=1;MQM=43.6452;MQMR=48.4886;NS=4;NUMALT=1;ODDS=9.57418;PAIRED=0.322581;PAIREDR=0.511364;PAO=0;PQA=0;PQR=0;PRO=0;QA=1155;QR=3217;RO=88;RPL=12;RPP=6.44263;RPPR=17.2236;RPR=19;RUN=1;SAF=18;SAP=4.76149;SAR=13;SRF=30;SRP=22.3561;SRR=58;TYPE=snp;technology.Illumina=1	GT:DP:RO:QR:AO:QA:GL	0/1:40:30:1119:10:381:-19.5199,0,-84.6158	0/1:38:26:914:12:428:-23.9357,0,-67.3768	0/1:18:14:518:4:153:-7.78315,0,-39.0649	0/1:23:18:666:5:193:-10.1182,0,-48.9653
+gnl|UG|Ta#S58861868	789	.	T	C	288.497	.	AB=0.262136;ABP=53.6288;AC=4;AF=0.5;AN=8;AO=27;CIGAR=1X;DP=103;DPB=103;DPRA=0;EPP=5.02092;EPPR=19.4678;GTI=0;LEN=1;MEANALT=1;MQM=46.3333;MQMR=46.9737;NS=4;NUMALT=1;ODDS=7.81504;PAIRED=0.444444;PAIREDR=0.447368;PAO=0;PQA=0;PQR=0;PRO=0;QA=932;QR=2888;RO=76;RPL=27;RPP=61.6401;RPPR=80.269;RPR=0;RUN=1;SAF=11;SAP=5.02092;SAR=16;SRF=32;SRP=7.12467;SRR=44;TYPE=snp;technology.Illumina=1	GT:DP:RO:QR:AO:QA:GL	0/1:34:27:1047:7:258:-12.343,0,-79.0918	0/1:33:24:888:9:294:-16.0112,0,-64.6095	0/1:15:11:418:4:139:-7.86508,0,-31.1628	0/1:21:14:535:7:241:-13.8931,0,-39.0865
+gnl|UG|Ta#S58861868	796	.	AAGC	GGGA	347.21	.	AB=0.280899;ABP=40.1205;AC=4;AF=0.5;AN=8;AO=25;CIGAR=2X1M1X;DP=89;DPB=89.75;DPRA=0;EPP=10.0459;EPPR=13.8677;GTI=1;LEN=4;MEANALT=2;MQM=41.56;MQMR=48.2444;NS=4;NUMALT=1;ODDS=9.57947;PAIRED=0.24;PAIREDR=0.488889;PAO=0;PQA=0;PQR=34;PRO=1;QA=868;QR=1723;RO=45;RPL=25;RPP=57.2971;RPPR=100.727;RPR=0;RUN=1;SAF=17;SAP=10.0459;SAR=8;SRF=15;SRP=13.8677;SRR=30;TYPE=complex;technology.Illumina=1	GT:DP:RO:QR:AO:QA:GL	0/1:31:17:645:8:299:-17.1226,0,-48.1088	0/1:28:13:516:9:275:-16.6666,0,-37.1959	0/1:13:7:261:3:108:-6.08173,0,-21.5188	0/1:17:8:301:5:186:-12.4084,0,-21.3491

data/test/data/S58861868/header.txt

@@ -0,0 +1,9 @@
+@SQ	SN:gnl|UG|Ta#S58861868	LN:843
+@PG	ID:bwa	PN:bwa	VN:0.5.9-r26-dev
+@PG	ID:bwa-527B2A44	PN:bwa	VN:0.5.9-r26-dev
+@PG	ID:bwa-1257F415	PN:bwa	VN:0.5.9-r26-dev
+@PG	ID:bwa-3214D905	PN:bwa	VN:0.5.9-r26-dev
+@RG	ID:LIB1721	PL:Illumina	LB:LIB1721	SM:AVS
+@RG	ID:LIB1722	PL:Illumina	LB:LIB1722	SM:Yr15
+@RG	ID:LIB1716	PL:Illumina	LB:LIB1716	SM:R2
+@RG	ID:LIB1719	PL:Illumina	LB:LIB1719	SM:S2

data/test/data/bfr_out_test.csv

@@ -1,5 +1,5 @@
-LIB1721	LIB1722	LIB1716	LIB1719	gnl|UG|Ta#S22380157	g	210	C	1.06	144	136	LIB1722	0.17	0.18	24	24
-LIB1721	LIB1722	LIB1716	LIB1719	gnl|UG|Ta#S22380157	g	297	A	0.8	172	164	LIB1722	0.2	0.16	34	26
-LIB1721	LIB1722	LIB1716	LIB1719	gnl|UG|Ta#S22380157	t	300	C	0.84	173	168	LIB1722	0.18	0.15	32	26
-LIB1721	LIB1722	LIB1716	LIB1719	gnl|UG|Ta#S22380157	g	645	A	0.4	78	87	LIB1721	0.28	0.71	22	62
-LIB1721	LIB1722	LIB1716	LIB1719	gnl|UG|Ta#S22380157	a	674	G	0.36	49	55	LIB1722	0.45	0.16	22	9
+LIB1721	LIB1722	LIB1716	LIB1719	gnl|UG|Ta#S22380157	g	210	C	1.34	171	175	LIB1722	0.14	0.19	24	33
+LIB1721	LIB1722	LIB1716	LIB1719	gnl|UG|Ta#S22380157	g	297	A	0.73	177	174	LIB1722	0.2	0.14	35	25
+LIB1721	LIB1722	LIB1716	LIB1719	gnl|UG|Ta#S22380157	t	300	C	0.76	178	176	LIB1722	0.18	0.14	32	24
+LIB1721	LIB1722	LIB1716	LIB1719	gnl|UG|Ta#S22380157	g	645	A	0.52	60	69	LIB1721	0.37	0.71	22	49
+LIB1721	LIB1722	LIB1716	LIB1719	gnl|UG|Ta#S22380157	a	674	G	0.57	42	46	LIB1722	0.38	0.22	16	10

data/test/data/headerMergeed.txt

@@ -0,0 +1,9 @@
+@SQ	SN:gnl|UG|Ta#S22380157	LN:859
+@PG	ID:bwa	PN:bwa	VN:0.5.9-r26-dev
+@PG	ID:bwa-527B2A44	PN:bwa	VN:0.5.9-r26-dev
+@PG	ID:bwa-1257F415	PN:bwa	VN:0.5.9-r26-dev
+@PG	ID:bwa-3214D905	PN:bwa	VN:0.5.9-r26-dev
+@RG	ID:LIB1721	PL:Illumina	LB:LIB1721	SM:AVS
+@RG	ID:LIB1722	PL:Illumina	LB:LIB1722	SM:Yr15
+@RG	ID:LIB1716	PL:Illumina	LB:LIB1716	SM:R2
+@RG	ID:LIB1719	PL:Illumina	LB:LIB1719	SM:S2

data/test/data/headerS2238015

@@ -0,0 +1 @@
+@SQ	SN:gnl|UG|Ta#S22380157	LN:859

data/test/test_bfr.rb

@@ -1,11 +1,16 @@
+
 $: << File.expand_path(File.dirname(__FILE__) + '/../lib')
 $: << File.expand_path('.')
 path= File.expand_path(File.dirname(__FILE__) + '/../lib/bioruby-polyploid-tools.rb')
 
+tmp_verb = $VERBOSE
+$VERBOSE=nil
 #puts path
 require path
 require 'bio-samtools'
 require "test/unit"
+$VERBOSE=tmp_verb
+
 
 class TestPolyploidTools < Test::Unit::TestCase
 
@@ -40,7 +45,7 @@ class TestPolyploidTools < Test::Unit::TestCase
     reg="gnl|UG|Ta#S22380157"
     region = @fasta_db.index.region_for_entry(reg).to_region
     min_cov=20
-    puts region.to_s
+    #puts region.to_s
     
     #puts @bam_a.methods
     ref_seq=@fasta_db.fetch_sequence(region)
@@ -56,27 +61,14 @@ class TestPolyploidTools < Test::Unit::TestCase
     called_2 = reg_b.called
     
     snps_tot = Bio::Sequence.snps_between(cons_1, cons_2)
-    block_size = 1000
-    snps_per_1k_1   = (block_size * snps_1.to_f   ) / region.size
-    snps_per_1k_2   = (block_size * snps_2.to_f   ) / region.size
-    snps_per_1k_tot = (block_size * snps_tot.to_f ) / region.size
-
-    
-
-    #puts "#{region.entry}\t#{region.size}\t"
-    #puts "#{snps_1}\t#{called_1}\t#{snps_per_1k_1}\t"
-    #puts "#{snps_2}\t#{called_2}\t#{snps_per_1k_2}\t"
-    #puts "#{snps_tot}\t#{snps_per_1k_tot}\n"
-    
-    
+    #block_size = 1000
+    #snps_per_1k_1   = (block_size * snps_1.to_f   ) / region.size
+    #snps_per_1k_2   = (block_size * snps_2.to_f   ) / region.size
+    #snps_per_1k_tot = (block_size * snps_tot.to_f ) / region.size
+        
     snps_tot = Bio::Sequence.snps_between(cons_1, cons_2)
     snps_to_ref = Bio::Sequence.snps_between(cons_1, ref_seq)
-    #puts ">ref\n#{ref_seq}"
-    #puts ">a\n#{cons_1}"
-    #puts ">b\n#{cons_2}"
-    #puts "SNPS between: #{snps_tot}"
-    #puts "SNPS ref: #{snps_to_ref}"
-    #puts "SNPS call: #{snps_to_ref}"
+
     assert_equal(ref_seq.to_s, "acgcttgaccttaggcctatttaggtgacactatagaacaagtttgtacaaaaaagcaggctggtaccggtccggaattcccgggatatcgtcgacccacgcgtccgcgtccgaccagcacaaacaagactgtactctgggctcctctgactccgtgtcttgctaaaatatctttggtcgactcgttgcgaggttgatcagatggcggaggaagcgaagcaggatgtggcgccacccgcgccggagccgaccgaggacgtcgcggacgagaaggtggcggttccgtcgccggaggagtctaaggccctcgttgtcgccgagaatgacgctgagaagcctgcagctacagggggctcacacgaacgagatgctctgctcacgagggtcgcgaccgagaagaggatttcgctgatcaaggcatgggaggagaacgagaaggccaaagccgagaacaaggccgtgaagttgctggcggacatcacctcgtgggagaactccaaggccgcggaactggaagccgagctcaagaagatgcaagagcagctggagaagaagaaggcgcgctgcgtggagaagctcaagaacagcgccgcgacggtgcacaaagaggcggaangagaagcgtgccgcggcggaagcgcggcacggcgaggagatcgtcgcggcggaggagaccgccgccaagtaccgcgccaagggtgaagcgccgaagaagctgctcttcggcagaagatagatatcgcttcatcttcagcttctctctgtttgaccgnttgcatgtctcctgcccatggcatcacttgtgtatttatctttgggggngatcttagtttgtatggtatcatcaaatgcgtcgtga")
     assert_equal(cons_1.to_s , "acgcttgaccttaggcctatttaggtgacactatagaacaagtttgtacaaaaaagcaggctggtaccggtccggaattcccgggatatcgtcgacccacgcgtccgcgtccgaccagcacaaacaagactgtactctgggctcctctgactccgtgtcttgctaaaatatytttggtcgactcgttgcgaggttgatcagatggcggaggaagcgaagcaggatgtggcgccacccgcgccggagccgaccgaggacgtcgcggacgagaaggcggcggttccgtcgccggaggagtctaaggccctsgttgtcgccgagaatgacgcygagaagcctgcagctacagggggctcacacgaacgagatgctctgctcacgagggtygcgaccgagaagaggatttcgctgatcaaggcatgggaggagaaygagaaggccaaagccgagaacaaggccgtgaagttgctggcggacatcacctcgtgggagaactccaaggccgcggaactggaagccgagctcaagaagatgcaagagcagctggagaagaagaaggcgcgctgcgtggagaagctcaagaacagcgccgcgacggtgcacaaagaggcgraaggagaagcgtgccgcggcggaagygcggcrcggcgaggagatcgtcgcggcggaggagaccgccgccaagtaccgcgccaagggtgaggcgccgaagaagctgctcttcggcagaggatagatatcgcttcatcttcagcttctctctgtttgaccgnttgcatgtctcctgcccatggcatcacttgtgtatttatctttgggggngatcttagtttgtatggtatcatcaaatgcgtcgtga")  
     assert_equal(cons_2.to_s , "acgcttgaccttaggcctatttaggtgacactatagaacaagtttgtacaaaaaagcaggctggtaccggtccggaattcccgggatatcgtcgacccacgcgtccgcgtccgaccagcacaaacaagactgtactctgggctcctctgactccgtgtcttgctaaaatatytttggtcgactcgttgcgaggttgatcagatggcggasgaagcgaagcaggatgtggcgccacccgcgccggagccgaccgaggacgtcgcggacgagaaggcggcggttccgtcgccggaggartcyaaggccctsgttgtcgccgagaatgacgcygagaagcctgcagctacagggggctcacacgaacgagatgctctgctcacgagggtygcgaccgagaagaggatttcgctgatcaaggcatgggaggagaaygagaaggccaaagccgagaacaaggccgtgaagttgctggcggacatcacctcgtgggagaactccaaggccgcggaactggaagccgagctcaagaagatgcaagagcagctggagaagaagaaggcgcgctgcgtggagaagctcaagaacagcgccgcgacggtgcacaaagaggcgraaggagaagcgtgccgcggcggaagygcggcgcggcgaggagatcgtcgcggcggaggagrccgccgccaagtaccgcgccaagggtgaggcgccgaagaagctgctcttcggcagaagatagatatcgcttcatcttcagcttctctctgtttgaccgnttgcatgtctcctgcccatggcatcacttgtgtatttatctttgggggngatcttagtttgtatggtatcatcaaatgcgtcgtga")
@@ -108,7 +100,7 @@ class TestPolyploidTools < Test::Unit::TestCase
     @fasta_db.index.entries.each do | r |
       i = i  + 1
        
-      reg = container.process_region({:region => r.get_full_region.to_s,:output_file => output_file , :min_cov => 5} )
+      reg = container.process_region({:A => true, :q => 37, :region => r.get_full_region.to_s,:output_file => output_file , :min_cov => 5} )
       #puts reg.inspect
     end
     
@@ -116,21 +108,21 @@ class TestPolyploidTools < Test::Unit::TestCase
     
     bases_1 = Array.new
     bases_2 = Array.new
-    bases_1  << {:A=>0, :C=>24, :G=>120, :T=>0}
-    bases_2  << {:A=>0, :C=>24, :G=>112, :T=>0}
-    bases_1  << {:A=>34, :C=>0, :G=>138, :T=>0}
-    bases_2  << {:A=>26, :C=>0, :G=>138, :T=>0}
-    bases_1  << {:A=>0, :C=>32, :G=>0, :T=>141}
-    bases_2  << {:A=>0, :C=>26, :G=>0, :T=>142}
-    bases_1  << {:A=>22, :C=>0, :G=>56, :T=>0}
-    bases_2  << {:A=>62, :C=>0, :G=>25, :T=>0}
-    bases_1  << {:A=>27, :C=>0, :G=>22, :T=>0}
-    bases_2  << {:A=>46, :C=>0, :G=>9, :T=>0}
+    bases_1  << {:A=>0, :C=>24, :G=>147, :T=>0}
+    bases_2  << {:A=>0, :C=>33, :G=>142, :T=>0}
+    bases_1  << {:A=>35, :C=>0, :G=>142, :T=>0}
+    bases_2  << {:A=>25, :C=>0, :G=>149, :T=>0}
+    bases_1  << {:A=>0, :C=>32, :G=>0, :T=>146}
+    bases_2  << {:A=>0, :C=>24, :G=>0, :T=>152}
+    bases_1  << {:A=>22, :C=>0, :G=>38, :T=>0}
+    bases_2  << {:A=>49, :C=>0, :G=>20, :T=>0}
+    bases_1  << {:A=>26, :C=>0, :G=>16, :T=>0}
+    bases_2  << {:A=>36, :C=>0, :G=>10, :T=>0}
     i = 0
     with_bfr.each do | pos |
-      puts pos
-      assert_equal(reg.bases_bulk_1[pos - 1 ] , bases_1[i] )
-      assert_equal(reg.bases_bulk_2[pos - 1 ] , bases_2[i] )
+      #puts pos
+      assert_equal(bases_1[i], reg.bases_bulk_1[pos - 1 ] )
+      assert_equal(bases_2[i], reg.bases_bulk_2[pos - 1 ] )
       i += 1
     end
    

data/test/test_blast.rb

@@ -0,0 +1,47 @@
+$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
+$: << File.expand_path('.')
+path= File.expand_path(File.dirname(__FILE__) + '/../lib/bioruby-polyploid-tools.rb')
+
+#puts path
+require path
+require "test/unit"
+
+class TestBlast < Test::Unit::TestCase
+  Query  = File.dirname(__FILE__) + '/data/' + "BS00068396_51.fa"
+  Target = File.dirname(__FILE__) + '/data/' + "BS00068396_51_contigs.fa"
+  Blast_file = File.dirname(__FILE__) + '/data/' + "BS00068396_51_blast.tab"
+  #Set up the paths
+  def setup
+    File.expand_path(File.dirname(__FILE__) + '/data/')
+  end
+  
+  
+  
+  def test_blast_to_exo
+    lines = File.readlines(Blast_file)
+    expected = [
+    "BS00068396_51 0 101 + 2AS_5222932 3015 2914 - 99",
+    "BS00068396_51 0 101 + 2DS_5334799 6812 6913 + 99",
+    "BS00068396_51 0 101 + 2BS_5245544 4549 4651 + 87",
+    "BS00068396_51 101 0 - 2BS_5163353 7425 7323 - 87"]
+
+    expected_v = [
+      "M 101 101", 
+      "M 101 101",
+      "M 69 69 G 0 1 M 32 32",
+      "M 69 69 G 1 0 M 32 32"]
+
+    lines.each_with_index do |line , i|
+      tmp =  Bio::DB::Blast.to_sugar(line)
+      assert_equal(tmp, expected[i], "Error in line #{i} of the SUGAR")
+      tmp =   Bio::DB::Blast.to_vulgar(line)
+      assert_equal(tmp, expected_v[i], "Error in line #{i} of the Vulgar")
+
+      tmp =   Bio::DB::Blast.to_exo(line)
+      puts tmp
+    
+    end
+    
+  end
+  
+end

data/test/test_exonearate.rb

@@ -6,22 +6,17 @@ path= File.expand_path(File.dirname(__FILE__) + '/../lib/bioruby-polyploid-tools
 require path
 require "test/unit"
 
-class TestPolyploidTools < Test::Unit::TestCase
-  Query=File.dirname(__FILE__) + '/data/'+"BS00068396_51.fa"
-  Target=File.dirname(__FILE__) + '/data/'+"BS00068396_51_contigs.fa"
+class TestExonerate < Test::Unit::TestCase
+  Query  = File.dirname(__FILE__) + '/data/'+"BS00068396_51.fa"
+  Target = File.dirname(__FILE__) + '/data/'+"BS00068396_51_contigs.fa"
   #Set up the paths
   def setup
     File.expand_path(File.dirname(__FILE__) + '/data/')
-    
-  
   end
   
-  def teardown
-    
-  end
+  
   
   def test_simple_align_array
- #   puts $LOAD_PATH
     alignments = Bio::DB::Exonerate.align({:query=>Query, :target=>Target})
     assert(alignments.size == 4, "The count of alignments should be 4, it was #{alignments.size}")
   end

data/test/test_snp_parsing.rb

@@ -6,44 +6,29 @@ path= File.expand_path(File.dirname(__FILE__) + '/../lib/bioruby-polyploid-tools
 require path
 require "test/unit"
 
-class TestPolyploidTools < Test::Unit::TestCase
+class TestSNPparsing < Test::Unit::TestCase
 
   #Set up the paths
   def setup
-    @data = File.expand_path(File.dirname(__FILE__) + "/data")
-    
-  end
-  
-  def teardown
-    
-  end
-  
-  
-  def test_default
- #   puts $LOAD_PATH
-    assert(true, "Unit test test")
+    @data = File.expand_path(File.dirname(__FILE__) + "/data")    
   end
-  
+
   def test_snp_sequence
     snp = Bio::PolyploidTools::SNPSequence.parse("BS00068396_51,2A,CGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTA[T/C]ATGCAGGATCTTGATTAGTCGTGTGAACAACTGAAATTTGAGCGCCACAA")
     assert(snp.gene == "BS00068396_51" )
     assert(snp.chromosome == "2A")
-   
     assert(snp.sequence_original == "CGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTA[T/C]ATGCAGGATCTTGATTAGTCGTGTGAACAACTGAAATTTGAGCGCCACAA")
-    
     assert_equal(snp.position ,  51, "Position isnt parsed #{snp.position}")
     assert_equal(snp.original , "T", "ORiginal base not parsed, is #{snp.original}")
     assert_equal(snp.snp , "C")
-    
     assert(snp.template_sequence == "CGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTAYATGCAGGATCTTGATTAGTCGTGTGAACAACTGAAATTTGAGCGCCACAA", "#{snp.template_sequence}!=CGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTAYATGCAGGATCTTGATTAGTCGTGTGAACAACTGAAATTTGAGCGCCACAA")
-    #true
   end
 
   def test_mutant_snp
 
     ref=@data + "/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa"
-    
     fasta_reference_db = Bio::DB::Fasta::FastaFile.new({:fasta=>ref})
+    fasta_reference_db.index
     fasta_reference_db.load_fai_entries 
     
     snp = Bio::PolyploidTools::SNPMutant.parse("IWGSC_CSS_1AL_scaff_1455974,Kronos2281,127,C,T")
@@ -51,12 +36,12 @@ class TestPolyploidTools < Test::Unit::TestCase
     assert_equal(snp.contig, "IWGSC_CSS_1AL_scaff_1455974")
     assert_equal(snp.chromosome, "1A", "The chromosome wasnt parsed: #{snp.chromosome}")
     assert_equal(snp.position, 127, "The position is not parsed: #{snp.position}")
-    
+    #snp.setTemplateFromFastaFile(fasta_reference_db, flanking_size = 100)
     region = fasta_reference_db.index.region_for_entry(snp.contig).get_full_region
     snp.full_sequence = fasta_reference_db.fetch_sequence(region)
 
-    assert_equal(snp.template_sequence, "actcgatcgtcagcacccgctggaacttggggaacgtcttgaacgccgcaagcaccggggcgtcctctgactgtatgagcacgcgctgcttacaggtctcYttgtcgtacccggacttgacaagcgctttggagaccgcatccaccacgtcaaggcttctggctataaggtacgtagcatgctgcactcggtaggtacaaga")
-    assert_equal(snp.sequence_original, "actcgatcgtcagcacccgctggaacttggggaacgtcttgaacgccgcaagcaccggggcgtcctctgactgtatgagcacgcgctgcttacaggtctc[C/T]ttgtcgtacccggacttgacaagcgctttggagaccgcatccaccacgtcaaggcttctggctataaggtacgtagcatgctgcactcggtaggtacaaga")
+    assert_equal(snp.template_sequence, "actcgatcgtcagcacccgctggaacttggggaacgtcttgaacgccgcaagcaccggggcgtcctctgactgtatgagcacgcgctgcttacaggtctcYttgtcgtacccggacttgacaagcgctttggagaccgcatccaccacgtcaaggcttctggctataaggtacgtagcatgctgcactcggtaggtacaag")
+    assert_equal(snp.sequence_original, "actcgatcgtcagcacccgctggaacttggggaacgtcttgaacgccgcaagcaccggggcgtcctctgactgtatgagcacgcgctgcttacaggtctc[C/T]ttgtcgtacccggacttgacaagcgctttggagaccgcatccaccacgtcaaggcttctggctataaggtacgtagcatgctgcactcggtaggtacaag")
     assert_equal(snp.position, 101)
     assert_equal(snp.original, "C")
     assert_equal(snp.snp, "T")
@@ -64,5 +49,40 @@ class TestPolyploidTools < Test::Unit::TestCase
     
   end
 
+  def test_reference_snp
+
+    ref=@data + "/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa"
+    fasta_reference_db = Bio::DB::Fasta::FastaFile.new({:fasta=>ref})
+    
+    fasta_reference_db.load_fai_entries 
+    
+    snp = Bio::PolyploidTools::SNP.parse("IWGSC_CSS_1AL_scaff_1455974,C,127,T,1A")
+    assert_equal(snp.gene , "IWGSC_CSS_1AL_scaff_1455974", "The original name was not parsed: #{snp.gene}")
+    assert_equal("1A", snp.chromosome, "The chromosome wasnt parsed: #{snp.chromosome}")
+    assert_equal(127, snp.position, "The position is not parsed: #{snp.position}")
+    snp.setTemplateFromFastaFile(fasta_reference_db, flanking_size = 100)
+    assert_equal("actcgatcgtcagcacccgctggaacttggggaacgtcttgaacgccgcaagcaccggggcgtcctctgactgtatgagcacgcgctgcttacaggtctcYttgtcgtacccggacttgacaagcgctttggagaccgcatccaccacgtcaaggcttctggctataaggtacgtagcatgctgcactcggtaggtacaaga",     snp.template_sequence)
+    assert_equal("actcgatcgtcagcacccgctggaacttggggaacgtcttgaacgccgcaagcaccggggcgtcctctgactgtatgagcacgcgctgcttacaggtctc[C/T]ttgtcgtacccggacttgacaagcgctttggagaccgcatccaccacgtcaaggcttctggctataaggtacgtagcatgctgcactcggtaggtacaag", snp.to_polymarker_sequence(100))
+    assert_equal(101,snp.position)
+    assert_equal("C",snp.original)
+    assert_equal("T",snp.snp)
+    
+    flanking_size = 3
+
+    snp = Bio::PolyploidTools::SNP.parse("IWGSC_CSS_1DL_scaff_2258883,A,12498,C,1D")
+    snp.setTemplateFromFastaFile(fasta_reference_db, flanking_size = flanking_size)
+    assert_equal(4,snp.position)
+    assert_equal("A",snp.original)
+    assert_equal("C",snp.snp)
+    assert_equal("gatM", snp.template_sequence)
+
+    snp = Bio::PolyploidTools::SNP.parse("IWGSC_CSS_1BL_scaff_3810460,G,1,T,1B")
+    snp.setTemplateFromFastaFile(fasta_reference_db, flanking_size = flanking_size)
+    assert_equal(1,snp.position)
+    assert_equal("G",snp.original)
+    assert_equal("T",snp.snp)
+    assert_equal("Kaatt", snp.template_sequence)    
+  end
+
   
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 0.7.3
+  version: 0.8.0
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-08-10 00:00:00.000000000 Z
+date: 2018-01-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -16,50 +16,64 @@ dependencies:
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.4.3
+        version: 1.5.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.4.3
+        version: 1.5.1
 - !ruby/object:Gem::Dependency
   name: bio-samtools
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 2.0.4
+        version: 2.6.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 2.0.4
+        version: 2.6.2
 - !ruby/object:Gem::Dependency
-  name: rake
+  name: systemu
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 2.5.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 2.5.2
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '2.10'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '2.10'
 - !ruby/object:Gem::Dependency
-  name: jeweler
+  name: test-unit
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
-  type: :runtime
+  type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
@@ -67,60 +81,76 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: systemu
+  name: juwelier
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 2.5.2
-  type: :runtime
+        version: '0'
+  type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 2.5.2
-description: Repository of tools developed in TGAC and Crop Genetics in JIC to work
-  with polyploid wheat
-email: ricardo.ramirez-gonzalez@tgac.ac.uk
+        version: '0'
+description: Repository of tools developed at Crop Genetics in JIC to work with polyploid
+  wheat
+email: ricardo.ramirez-gonzalez@jic.ac.uk
 executables:
 - bfr.rb
+- blast_triads.rb
+- blast_triads_promoters.rb
 - count_variations.rb
 - filter_blat_by_target_coverage.rb
 - filter_exonerate_by_identity.rb
 - find_best_blat_hit.rb
 - find_best_exonerate.rb
+- find_homoeologue_variations.rb
+- get_longest_hsp_blastx_triads.rb
 - hexaploid_primers.rb
 - homokaryot_primers.rb
+- mafft_triads.rb
+- mafft_triads_promoters.rb
 - map_markers_to_contigs.rb
 - markers_in_region.rb
 - polymarker.rb
+- polymarker_capillary.rb
 - snp_position_to_polymarker.rb
 - snps_between_bams.rb
+- vcfLineToTable.rb
 extensions: []
 extra_rdoc_files:
 - README
 - README.md
 files:
+- ".travis.yml"
 - Gemfile
-- Gemfile.lock
 - README
 - README.md
 - Rakefile
 - VERSION
 - bin/bfr.rb
+- bin/blast_triads.rb
+- bin/blast_triads_promoters.rb
 - bin/count_variations.rb
 - bin/filter_blat_by_target_coverage.rb
 - bin/filter_exonerate_by_identity.rb
 - bin/find_best_blat_hit.rb
 - bin/find_best_exonerate.rb
+- bin/find_homoeologue_variations.rb
+- bin/get_longest_hsp_blastx_triads.rb
 - bin/hexaploid_primers.rb
 - bin/homokaryot_primers.rb
+- bin/mafft_triads.rb
+- bin/mafft_triads_promoters.rb
 - bin/map_markers_to_contigs.rb
 - bin/markers_in_region.rb
 - bin/polymarker.rb
+- bin/polymarker_capillary.rb
 - bin/snp_position_to_polymarker.rb
 - bin/snps_between_bams.rb
+- bin/vcfLineToTable.rb
 - bio-polyploid-tools.gemspec
 - conf/defaults.rb
 - conf/primer3_config/dangle.dh
@@ -162,21 +192,29 @@ files:
 - lib/bio/PolyploidTools/ChromosomeArm.rb
 - lib/bio/PolyploidTools/ExonContainer.rb
 - lib/bio/PolyploidTools/Marker.rb
+- lib/bio/PolyploidTools/NoSNPSequence.rb
 - lib/bio/PolyploidTools/PrimerRegion.rb
 - lib/bio/PolyploidTools/SNP.rb
 - lib/bio/PolyploidTools/SNPMutant.rb
 - lib/bio/PolyploidTools/SNPSequence.rb
+- lib/bio/db/blast.rb
 - lib/bio/db/exonerate.rb
 - lib/bio/db/primer3.rb
 - lib/bioruby-polyploid-tools.rb
 - test/data/BS00068396_51.fa
+- test/data/BS00068396_51_blast.tab
 - test/data/BS00068396_51_contigs.aln
 - test/data/BS00068396_51_contigs.dnd
 - test/data/BS00068396_51_contigs.fa
+- test/data/BS00068396_51_contigs.nhr
+- test/data/BS00068396_51_contigs.nin
+- test/data/BS00068396_51_contigs.nsq
 - test/data/BS00068396_51_exonerate.tab
+- test/data/BS00068396_51_for_polymarker.fa
 - test/data/BS00068396_51_genes.txt
 - test/data/IWGSC_CSS_1AL_scaff_1455974.fa
 - test/data/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa
+- test/data/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa.fai
 - test/data/LIB1716.bam
 - test/data/LIB1716.bam.bai
 - test/data/LIB1719.bam
@@ -191,9 +229,31 @@ files:
 - test/data/PST130_reverse_primer.csv
 - test/data/S22380157.fa
 - test/data/S22380157.fa.fai
+- test/data/S22380157.vcf
+- test/data/S58861868/LIB1716.bam
+- test/data/S58861868/LIB1716.sam
+- test/data/S58861868/LIB1719.bam
+- test/data/S58861868/LIB1719.sam
+- test/data/S58861868/LIB1721.bam
+- test/data/S58861868/LIB1721.sam
+- test/data/S58861868/LIB1722.bam
+- test/data/S58861868/LIB1722.sam
+- test/data/S58861868/S58861868.fa
+- test/data/S58861868/S58861868.fa.fai
+- test/data/S58861868/S58861868.vcf
+- test/data/S58861868/header.txt
+- test/data/S58861868/merged.bam
+- test/data/S58861868/merged_reheader.bam
+- test/data/S58861868/merged_reheader.bam.bai
 - test/data/Test3Aspecific.csv
 - test/data/Test3Aspecific_contigs.fa
 - test/data/bfr_out_test.csv
+- test/data/headerMergeed.txt
+- test/data/headerS2238015
+- test/data/mergedLibs.bam
+- test/data/mergedLibsReheader.bam
+- test/data/mergedLibsSorted.bam
+- test/data/mergedLibsSorted.bam.bai
 - test/data/patological_cases5D.csv
 - test/data/primer_3_input_header_test
 - test/data/short_primer_design_test.csv
@@ -204,6 +264,7 @@ files:
 - test/data/test_primer3_error.csv
 - test/data/test_primer3_error_contigs.fa
 - test/test_bfr.rb
+- test/test_blast.rb
 - test/test_exon_container.rb
 - test/test_exonearate.rb
 - test/test_snp_parsing.rb
@@ -228,7 +289,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.4.7
+rubygems_version: 2.7.4
 signing_key: 
 specification_version: 4
 summary: Tool to work with polyploids, NGS and molecular biology