ex-199 (jebene) moved example test data to directory. added functional

tests and readme

examples/README.rst

@@ -0,0 +1,26 @@
+=================
+Example VCF Files
+=================
+The vcfs directory contains example VCF files to be used as input for merge.
+These files have been de-identified and represent 5 patients.
+
+Usage
+=====
+
+To use Jacquard with the example data, run the following commands. Note that
+examples/vcfs is the input directory for translate.
+
+:translate:
+``$jacquard translate examples/vcfs <output_dir>/translated [options]``
+
+:merge:
+``$jacquard merge <output_dir>/translated <output_dir>/merged.vcf [options]``
+
+:summarize:
+``$jacquard summarize <output_dir>/merged.vcf <output_dir>/summarized.vcf [options]``
+
+:expand:
+``$jacquard expand <output_dir>/summarized.vcf <output_dir>/expanded.txt [options]``
+
+
+Refer to Jacquard/README.rst for more usage details

examples/vcfs/case_A.varscan.indel.Somatic.hc.fpfilter.pass

@@ -0,0 +1,83 @@
+chrom	position	ref	var	normal_reads1	normal_reads2	normal_var_freq	normal_gt	tumor_reads1	tumor_reads2	tumor_var_freq	tumor_gt	somatic_status	variant_p_value	somatic_p_value	tumor_reads1_plus	tumor_reads1_minus	tumor_reads2_plus	tumor_reads2_minus	normal_reads1_plus	normal_reads1_minus	normal_reads2_plus	normal_reads2_minus
+chr1	7709312	A	-C	38	0	0%	A	33	10	23.26%	*/-C	Somatic	1.0	0.0010207317573943328	22	11	6	4	21	17	0	0
+chr1	26870348	G	-T	53	1	1.85%	G	48	16	25%	*/-T	Somatic	1.0	1.9867564167709578E-4	26	22	11	5	32	21	1	0
+chr1	51182740	G	-T	39	2	4.88%	G	35	11	23.91%	*/-T	Somatic	1.0	0.012349190253268048	23	12	5	6	18	21	2	0
+chr1	101916499	G	-T	30	1	3.23%	G	31	10	24.39%	*/-T	Somatic	1.0	0.01254466013036908	24	7	9	1	26	4	1	0
+chr1	112945845	T	+A	57	0	0%	T	51	14	21.54%	*/+A	Somatic	1.0	7.132546619682443E-5	30	21	7	7	30	27	0	0
+chr1	132138402	A	-T	54	1	1.82%	A	40	11	21.57%	*/-T	Somatic	1.0	0.0012623590667436354	30	10	8	3	39	15	1	0
+chr2	44205625	A	-T	30	0	0%	A	31	10	24.39%	*/-T	Somatic	1.0	0.002427998734910192	4	27	1	9	5	25	0	0
+chr2	52924308	G	-A	36	1	2.7%	G	24	13	35.14%	*/-A	Somatic	1.0	3.02450897978653E-4	4	20	1	12	9	27	0	1
+chr2	60390689	C	-A	41	2	4.65%	C	53	18	25.35%	*/-A	Somatic	1.0	0.0033294932244736612	24	29	6	12	15	26	1	1
+chr2	67081276	G	-A	42	0	0%	G	39	13	25%	*/-A	Somatic	1.0	2.1081438651582003E-4	16	23	5	8	18	24	0	0
+chr2	71441853	G	+T	27	1	3.57%	G	29	10	25.64%	*/+T	Somatic	1.0	0.015156394589508205	19	10	5	5	16	11	0	1
+chr2	79641859	C	-T	58	1	1.69%	C	35	30	46.15%	*/-T	Somatic	1.0	1.1426826336218384E-9	12	23	11	19	14	44	0	1
+chr2	106334265	C	-T	14	0	0%	C	28	13	31.71%	*/-T	Somatic	1.0	0.01214187078396288	9	19	9	4	7	7	0	0
+chr3	1924476	C	-T	19	1	5%	C	18	13	41.94%	*/-T	Somatic	1.0	0.0033961654320554444	15	3	10	3	16	3	1	0
+chr3	48351683	C	+A	23	0	0%	C	34	10	22.73%	*/+A	Somatic	1.0	0.010005282256524793	9	25	1	9	7	16	0	0
+chr3	67416612	C	-T	35	1	2.78%	C	35	29	45.31%	*/-T	Somatic	1.0	1.7573590301171389E-6	12	23	13	16	13	22	1	0
+chr3	70859762	G	-T	43	1	2.27%	G	44	13	22.81%	*/-T	Somatic	1.0	0.002250006409563025	22	22	7	6	21	22	1	0
+chr3	88786546	T	-A	41	0	0%	T	32	23	41.82%	*/-A	Somatic	1.0	2.1749889498232658E-7	4	28	5	18	11	30	0	0
+chr3	97286977	T	-A	21	1	4.55%	T	21	23	52.27%	*/-A	Somatic	1.0	7.372789013815278E-5	3	18	2	21	2	19	0	1
+chr3	99025568	G	-T	40	0	0%	G	31	13	29.55%	*/-T	Somatic	1.0	8.29577550193283E-5	20	11	6	7	28	12	0	0
+chr3	100876723	C	-T	46	2	4.17%	C	29	33	53.23%	*/-T	Somatic	1.0	7.738284466184111E-9	16	13	12	21	35	11	1	1
+chr4	31702115	G	-A	40	0	0%	G	27	21	43.75%	*/-A	Somatic	1.0	2.2416701842340325E-7	9	18	6	15	8	32	0	0
+chr4	78896712	C	-A	28	1	3.45%	C	23	10	30.3%	*/-A	Somatic	1.0	0.005661950122413702	22	1	9	1	25	3	1	0
+chr4	80949554	T	-C	49	0	0%	T	30	33	52.38%	*/-C	Somatic	1.0	3.386537878851014E-11	20	10	18	15	35	14	0	0
+chr4	98564005	C	+A	27	0	0%	C	27	12	30.77%	*/+A	Somatic	1.0	7.944125893556465E-4	20	7	8	4	18	9	0	0
+chr4	102759730	A	-T	48	0	0%	A	43	20	31.75%	*/-T	Somatic	1.0	2.5166731236631777E-6	14	29	6	14	18	30	0	0
+chr4	116349053	A	-T	16	0	0%	A	25	11	30.56%	*/-T	Somatic	1.0	0.009946493495317787	3	22	1	10	3	13	0	0
+chr4	130495799	A	-T	40	2	4.76%	A	54	20	27.03%	*/-T	Somatic	1.0	0.002068920652494651	31	23	13	7	23	17	1	1
+chr5	20344465	G	-T	45	2	4.26%	G	54	14	20.59%	*/-T	Somatic	1.0	0.010382868830551797	27	27	7	7	23	22	0	2
+chr5	22559456	T	-A	62	0	0%	T	74	24	24.49%	*/-A	Somatic	1.0	2.2117154817466507E-6	17	57	3	21	16	46	0	0
+chr5	29339946	C	-T	41	2	4.65%	C	51	21	29.17%	*/-T	Somatic	1.0	8.559867347142869E-4	33	18	10	11	23	18	1	1
+chr5	50700734	C	-A	43	0	0%	C	21	16	43.24%	*/-A	Somatic	1.0	4.776195954349567E-7	11	10	6	10	18	25	0	0
+chr5	64925351	G	-T	36	0	0%	G	49	13	20.97%	*/-T	Somatic	1.0	0.0015460585739194175	24	25	9	4	20	16	0	0
+chr5	67512667	C	-T	22	0	0%	C	31	10	24.39%	*/-T	Somatic	1.0	0.008771916613082957	30	1	8	2	19	3	0	0
+chr5	100501319	C	-T	48	2	4%	C	24	33	57.89%	*/-T	Somatic	1.0	4.892578318402007E-10	15	9	23	10	33	15	1	1
+chr5	101697789	T	-GG	44	1	2.22%	T	41	28	40.58%	*/-GG	Somatic	1.0	7.625776760524336E-7	26	15	19	9	22	22	1	0
+chr5	129745842	T	-G	36	0	0%	T	32	16	33.33%	*/-G	Somatic	1.0	3.530294806154502E-5	18	14	11	5	21	15	0	0
+chr5	133018872	A	-T	33	1	2.94%	A	37	13	26%	*/-T	Somatic	1.0	0.004097098714636477	14	23	6	7	17	16	1	0
+chr6	20050121	A	+T	55	1	1.79%	A	52	16	23.53%	*/+T	Somatic	1.0	2.51392366937448E-4	22	30	11	5	32	23	1	0
+chr6	25853328	T	-A	47	1	2.08%	T	38	15	28.3%	*/-A	Somatic	1.0	1.9688684659368053E-4	27	11	10	5	33	14	1	0
+chr6	35018736	G	-TTTTTTTTT	42	2	4.55%	G	46	14	23.33%	*/-TTTTTTTTT	Somatic	1.0	0.007121547816795037	36	10	8	6	36	6	2	0
+chr6	90703143	A	-T	27	1	3.57%	A	25	8	24.24%	*/-T	Somatic	1.0	0.024641292558094073	1	24	0	8	5	22	0	1
+chr6	117979197	G	-C	36	0	0%	G	51	22	30.14%	*/-C	Somatic	1.0	4.206969219053543E-5	26	25	14	8	27	9	0	0
+chr6	127293518	A	-T	19	1	5%	A	16	11	40.74%	*/-T	Somatic	1.0	0.005323144556318262	13	3	8	3	13	6	1	0
+chr6	134456960	G	+A	52	0	0%	G	30	19	38.78%	*/+A	Somatic	1.0	1.1565019209588297E-7	14	16	12	7	30	22	0	0
+chr7	18088405	A	-C	41	1	2.38%	A	59	18	23.38%	*/-C	Somatic	1.0	0.0015019805818474127	25	34	13	5	24	17	1	0
+chr7	21840317	C	-T	51	0	0%	C	52	16	23.53%	*/-T	Somatic	1.0	5.462096095957074E-5	29	23	10	6	26	25	0	0
+chr7	65759119	T	-A	23	0	0%	T	22	10	31.25%	*/-A	Somatic	1.0	0.002205648508810455	9	13	2	8	15	8	0	0
+chr7	73389136	C	-A	45	1	2.17%	C	50	15	23.08%	*/-A	Somatic	1.0	0.001248926040882566	25	25	7	8	28	17	1	0
+chr7	100059377	C	-T	49	2	3.92%	C	50	21	29.58%	*/-T	Somatic	1.0	1.8664294533426605E-4	15	35	10	11	24	25	1	1
+chr7	102236114	C	+TCTGTCTACAGGCAAGGGTCT	29	0	0%	C	37	14	27.45%	*/+TCTGTCTACAGGCAAGGGTCT	Somatic	1.0	8.571456834808035E-4	19	18	6	8	18	11	0	0
+chr7	113957776	T	-G	28	0	0%	T	30	12	28.57%	*/-G	Somatic	1.0	0.001039404737670446	17	13	6	6	11	17	0	0
+chr8	18686549	G	-CC	52	2	3.7%	G	35	11	23.91%	*/-CC	Somatic	1.0	0.0029946520027459194	14	21	4	7	28	24	0	2
+chr8	20876228	G	+A	25	0	0%	G	25	11	30.56%	*/+A	Somatic	1.0	0.0014370095632324038	16	9	6	5	16	9	0	0
+chr8	21826486	C	-A	25	1	3.85%	C	9	14	60.87%	*/-A	Somatic	1.0	1.3796344398196046E-5	0	9	0	14	4	21	0	1
+chr8	35397880	T	+C	14	0	0%	T	21	8	27.59%	*/+C	Somatic	1.0	0.0295992622171097	1	20	0	8	0	14	0	0
+chr8	53950232	G	-T	29	1	3.33%	G	30	14	31.82%	*/-T	Somatic	1.0	0.0020167573487245684	28	2	8	6	24	5	1	0
+chr8	64845385	C	-A	15	0	0%	C	21	9	30%	*/-A	Somatic	1.0	0.01614505211842309	9	12	5	4	3	12	0	0
+chr8	77295887	C	-A	29	0	0%	C	25	11	30.56%	*/-A	Somatic	1.0	6.71239086880917E-4	7	18	5	6	7	22	0	0
+chr8	77399738	C	+A	48	1	2.04%	C	43	12	21.82%	*/+A	Somatic	1.0	0.001875963443162974	20	23	5	7	26	22	1	0
+chr8	77574046	G	-A	57	0	0%	G	45	15	25%	*/-A	Somatic	1.0	1.6846300996665185E-5	22	23	4	11	29	28	0	0
+chr8	105811749	C	+A	40	0	0%	C	40	15	27.27%	*/+A	Somatic	1.0	1.0781121696378358E-4	23	17	9	6	19	21	0	0
+chr8	107089323	C	+G	60	0	0%	C	56	21	27.27%	*/+G	Somatic	1.0	1.3821558229860335E-6	31	25	9	12	25	35	0	0
+chr8	108116652	C	-T	32	1	3.03%	C	37	14	27.45%	*/-T	Somatic	1.0	0.0030955856955032523	20	17	8	6	20	12	0	1
+chr8	112867306	C	-T	24	1	4%	C	30	13	30.23%	*/-T	Somatic	1.0	0.008056201297461556	16	14	9	4	13	11	0	1
+chr8	116313436	C	-T	35	1	2.78%	C	37	10	21.28%	*/-T	Somatic	1.0	0.012627278775344636	27	10	5	5	23	12	1	0
+chr9	6555883	C	+T	46	0	0%	C	38	13	25.49%	*/+T	Somatic	1.0	1.0218006310078289E-4	24	14	8	5	28	18	0	0
+chr9	31854704	A	-T	39	0	0%	A	24	11	31.43%	*/-T	Somatic	1.0	9.981905197325766E-5	22	2	11	0	30	9	0	0
+chr9	67947452	A	-T	49	2	3.92%	A	25	9	26.47%	*/-T	Somatic	1.0	0.003461368262735815	8	17	4	5	10	39	0	2
+chr9	84369497	G	-T	73	1	1.35%	G	81	25	23.58%	*/-T	Somatic	1.0	6.097435812427166E-6	56	25	15	10	41	32	0	1
+chr10	5684877	A	+T	49	0	0%	A	41	16	28.07%	*/+T	Somatic	1.0	1.5702164771424837E-5	20	21	6	10	21	28	0	0
+chr10	14060298	C	-A	54	1	1.82%	C	84	33	28.21%	*/-A	Somatic	1.0	7.585510612586361E-6	55	29	25	8	34	20	1	0
+chr10	19071710	A	-C	22	0	0%	A	31	10	24.39%	*/-C	Somatic	1.0	0.008771916613082957	19	12	7	3	13	9	0	0
+chr10	25924459	C	-A	44	1	2.22%	C	42	12	22.22%	*/-A	Somatic	1.0	0.0026742687018971208	25	17	8	4	30	14	0	1
+chr10	26215301	A	-T	38	0	0%	A	26	9	25.71%	*/-T	Somatic	1.0	7.272969694543718E-4	15	11	7	2	17	21	0	0
+chr10	42419832	G	-C	26	0	0%	G	18	8	30.77%	*/-C	Somatic	1.0	0.002076007708047738	2	16	2	6	4	22	0	0
+chr10	50556955	T	-A	34	0	0%	T	28	16	36.36%	*/-A	Somatic	1.0	2.4229488986166365E-5	1	27	2	14	3	31	0	0
+chr10	80291186	A	-T	33	0	0%	A	13	15	53.57%	*/-T	Somatic	1.0	5.307934002425958E-7	2	11	2	13	5	28	0	0
+chr10	91132855	A	-C	33	0	0%	A	37	16	30.19%	*/-C	Somatic	1.0	1.5356458666582992E-4	35	2	13	3	32	1	0	0
+chr10	101270340	G	+T	58	0	0%	G	50	23	31.51%	*/+T	Somatic	1.0	2.2981473902218676E-7	17	33	10	13	21	37	0	0
+chr10	101494755	A	-T	29	0	0%	A	30	11	26.83%	*/-T	Somatic	1.0	0.0014601161791085223	25	5	9	2	26	3	0	0
+chr10	115666922	G	-C	21	0	0%	G	23	8	25.81%	*/-C	Somatic	1.0	0.010482824026927818	11	12	5	3	9	12	0	0