diff test-data/samtools_stats_out1.tab @ 8:e28839a4b932 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"

--- a/test-data/samtools_stats_out1.tab	Thu Oct 17 02:21:23 2019 -0400
+++ b/test-data/samtools_stats_out1.tab	Tue Sep 28 16:17:39 2021 +0000
@@ -1,11 +1,11 @@
-# This file was produced by samtools stats (1.9+htslib-1.9) and can be plotted using plot-bamstats
+# This file was produced by samtools stats (1.12+htslib-1.12) and can be plotted using plot-bamstats
 # This file contains statistics for all reads.
-# The command line was:  stats --ref-seq reference.fa infile
+# The command line was:  stats --ref-seq reference.fa -@ 0 infile
 # CHK, Checksum	[2]Read Names	[3]Sequences	[4]Qualities
 # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)
 CHK	1bd20fd8	58ad2167	29883386
 # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
-SN	raw total sequences:	200
+SN	raw total sequences:	200	# excluding supplementary and secondary reads
 SN	filtered sequences:	0
 SN	sequences:	200
 SN	is sorted:	1
@@ -20,6 +20,7 @@
 SN	reads MQ0:	6	# mapped and MQ=0
 SN	reads QC failed:	0
 SN	non-primary alignments:	0
+SN	supplementary alignments:	0
 SN	total length:	50200	# ignores clipping
 SN	total first fragment length:	25100	# ignores clipping
 SN	total last fragment length:	25100	# ignores clipping
@@ -1094,6 +1095,258 @@
 GCC	249	25.00	23.00	21.00	31.00	0.00	0.00
 GCC	250	27.50	22.50	17.50	32.50	0.00	0.00
 GCC	251	13.50	20.50	36.50	29.50	0.00	0.00
+# ACGT content per cycle, read oriented. Use `grep ^GCT | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]
+GCT	1	22.45	32.65	31.63	13.27
+GCT	2	26.00	17.00	10.00	47.00
+GCT	3	34.00	25.00	9.00	32.00
+GCT	4	13.00	32.00	10.00	45.00
+GCT	5	37.00	24.00	10.00	29.00
+GCT	6	44.00	26.00	17.00	13.00
+GCT	7	28.00	13.00	32.00	27.00
+GCT	8	49.00	16.00	18.00	17.00
+GCT	9	19.00	35.00	16.00	30.00
+GCT	10	35.00	13.00	22.00	30.00
+GCT	11	18.00	15.00	29.00	38.00
+GCT	12	28.00	24.00	22.00	26.00
+GCT	13	29.00	17.00	19.00	35.00
+GCT	14	21.21	24.24	24.24	30.30
+GCT	15	23.00	20.00	25.00	32.00
+GCT	16	35.00	15.00	20.00	30.00
+GCT	17	29.00	26.00	13.00	32.00
+GCT	18	31.00	30.00	18.00	21.00
+GCT	19	30.00	26.00	21.00	23.00
+GCT	20	23.00	21.00	20.00	36.00
+GCT	21	36.00	18.00	19.00	27.00
+GCT	22	39.00	31.00	13.00	17.00
+GCT	23	30.30	21.21	11.11	37.37
+GCT	24	36.00	14.00	20.00	30.00
+GCT	25	38.00	23.00	17.00	22.00
+GCT	26	36.00	21.00	13.00	30.00
+GCT	27	32.00	18.00	22.00	28.00
+GCT	28	30.00	13.00	25.00	32.00
+GCT	29	30.00	28.00	23.00	19.00
+GCT	30	34.00	21.00	13.00	32.00
+GCT	31	33.00	29.00	14.00	24.00
+GCT	32	38.00	20.00	20.00	22.00
+GCT	33	27.00	23.00	15.00	35.00
+GCT	34	43.00	17.00	20.00	20.00
+GCT	35	35.00	23.00	22.00	20.00
+GCT	36	41.00	25.00	16.00	18.00
+GCT	37	38.00	18.00	18.00	26.00
+GCT	38	23.00	26.00	25.00	26.00
+GCT	39	22.00	41.00	19.00	18.00
+GCT	40	29.00	14.00	23.00	34.00
+GCT	41	29.00	27.00	20.00	24.00
+GCT	42	29.00	27.00	18.00	26.00
+GCT	43	38.00	28.00	16.00	18.00
+GCT	44	21.00	26.00	23.00	30.00
+GCT	45	38.00	25.00	18.00	19.00
+GCT	46	27.00	21.00	22.00	30.00
+GCT	47	40.00	28.00	18.00	14.00
+GCT	48	25.00	22.00	20.00	33.00
+GCT	49	26.00	33.00	10.00	31.00
+GCT	50	49.00	20.00	10.00	21.00
+GCT	51	29.00	29.00	13.00	29.00
+GCT	52	43.00	22.00	22.00	13.00
+GCT	53	19.00	27.00	27.00	27.00
+GCT	54	25.00	18.00	25.00	32.00
+GCT	55	32.00	22.00	17.00	29.00
+GCT	56	36.00	20.00	16.00	28.00
+GCT	57	28.00	24.00	23.00	25.00
+GCT	58	23.00	39.00	17.00	21.00
+GCT	59	33.00	21.00	26.00	20.00
+GCT	60	30.00	26.00	19.00	25.00
+GCT	61	23.00	23.00	25.00	29.00
+GCT	62	35.00	19.00	20.00	26.00
+GCT	63	26.00	25.00	29.00	20.00
+GCT	64	30.00	20.00	27.00	23.00
+GCT	65	38.00	17.00	21.00	24.00
+GCT	66	33.00	26.00	14.00	27.00
+GCT	67	35.00	21.00	21.00	23.00
+GCT	68	39.00	28.00	15.00	18.00
+GCT	69	38.00	18.00	22.00	22.00
+GCT	70	40.00	13.00	22.00	25.00
+GCT	71	29.00	41.00	19.00	11.00
+GCT	72	33.00	26.00	28.00	13.00
+GCT	73	31.00	18.00	24.00	27.00
+GCT	74	31.00	32.00	13.00	24.00
+GCT	75	46.00	10.00	21.00	23.00
+GCT	76	23.00	28.00	25.00	24.00
+GCT	77	35.00	20.00	19.00	26.00
+GCT	78	29.00	30.00	26.00	15.00
+GCT	79	24.00	25.00	27.00	24.00
+GCT	80	40.00	18.00	29.00	13.00
+GCT	81	18.00	26.00	26.00	30.00
+GCT	82	30.00	25.00	28.00	17.00
+GCT	83	36.00	25.00	14.00	25.00
+GCT	84	22.00	39.00	23.00	16.00
+GCT	85	42.00	20.00	21.00	17.00
+GCT	86	12.00	47.00	16.00	25.00
+GCT	87	45.00	15.00	19.00	21.00
+GCT	88	26.00	24.00	31.00	19.00
+GCT	89	26.00	25.00	29.00	20.00
+GCT	90	24.00	22.00	26.00	28.00
+GCT	91	29.00	30.00	24.00	17.00
+GCT	92	22.00	13.00	32.00	33.00
+GCT	93	29.00	40.00	13.00	18.00
+GCT	94	30.00	16.00	25.00	29.00
+GCT	95	31.31	35.35	17.17	16.16
+GCT	96	34.00	27.00	15.00	24.00
+GCT	97	32.00	27.00	25.00	16.00
+GCT	98	21.21	31.31	24.24	23.23
+GCT	99	27.00	37.00	21.00	15.00
+GCT	100	29.00	15.00	26.00	30.00
+GCT	101	27.00	34.00	25.00	14.00
+GCT	102	20.00	14.00	36.00	30.00
+GCT	103	32.00	26.00	16.00	26.00
+GCT	104	30.00	28.00	22.00	20.00
+GCT	105	35.00	35.00	19.00	11.00
+GCT	106	22.00	32.00	25.00	21.00
+GCT	107	19.19	33.33	26.26	21.21
+GCT	108	27.27	33.33	21.21	18.18
+GCT	109	19.00	29.00	24.00	28.00
+GCT	110	20.20	31.31	28.28	20.20
+GCT	111	25.25	33.33	22.22	19.19
+GCT	112	39.39	28.28	16.16	16.16
+GCT	113	21.21	24.24	31.31	23.23
+GCT	114	19.00	31.00	35.00	15.00
+GCT	115	32.00	23.00	25.00	20.00
+GCT	116	20.00	29.00	35.00	16.00
+GCT	117	31.00	21.00	21.00	27.00
+GCT	118	25.00	14.00	35.00	26.00
+GCT	119	21.00	31.00	24.00	24.00
+GCT	120	19.00	24.00	27.00	30.00
+GCT	121	24.24	36.36	20.20	19.19
+GCT	122	18.00	25.00	23.00	34.00
+GCT	123	25.00	48.00	10.00	17.00
+GCT	124	10.00	31.00	35.00	24.00
+GCT	125	27.00	24.00	22.00	27.00
+GCT	126	24.00	19.00	26.00	31.00
+GCT	127	26.00	16.00	22.00	36.00
+GCT	128	16.00	35.00	30.00	19.00
+GCT	129	24.00	27.00	26.00	23.00
+GCT	130	25.00	19.00	23.00	33.00
+GCT	131	17.00	40.00	24.00	19.00
+GCT	132	20.00	27.00	24.00	29.00
+GCT	133	15.00	34.00	33.00	18.00
+GCT	134	22.00	19.00	31.00	28.00
+GCT	135	17.00	28.00	26.00	29.00
+GCT	136	25.00	33.00	14.00	28.00
+GCT	137	21.00	22.00	30.00	27.00
+GCT	138	15.00	30.00	29.00	26.00
+GCT	139	19.00	32.00	22.00	27.00
+GCT	140	19.00	24.00	29.00	28.00
+GCT	141	21.00	24.00	25.00	30.00
+GCT	142	17.00	32.00	35.00	16.00
+GCT	143	23.00	23.00	28.00	26.00
+GCT	144	20.00	33.00	24.00	23.00
+GCT	145	20.00	26.00	24.00	30.00
+GCT	146	26.00	15.00	40.00	19.00
+GCT	147	23.00	23.00	30.00	24.00
+GCT	148	12.00	32.00	33.00	23.00
+GCT	149	27.00	24.00	23.00	26.00
+GCT	150	12.00	32.00	21.00	35.00
+GCT	151	22.00	29.00	34.00	15.00
+GCT	152	16.00	21.00	26.00	37.00
+GCT	153	24.00	20.00	34.00	22.00
+GCT	154	25.00	22.00	28.00	25.00
+GCT	155	21.00	28.00	17.00	34.00
+GCT	156	16.00	23.00	36.00	25.00
+GCT	157	23.00	34.00	20.00	23.00
+GCT	158	21.00	33.00	21.00	25.00
+GCT	159	19.00	15.00	44.00	22.00
+GCT	160	24.00	31.00	22.00	23.00
+GCT	161	13.00	28.00	40.00	19.00
+GCT	162	33.00	19.00	20.00	28.00
+GCT	163	23.00	26.00	31.00	20.00
+GCT	164	33.00	19.00	20.00	28.00
+GCT	165	13.00	16.00	37.00	34.00
+GCT	166	20.00	36.00	30.00	14.00
+GCT	167	17.00	28.00	25.00	30.00
+GCT	168	16.00	24.00	31.00	29.00
+GCT	169	21.00	23.00	21.00	35.00
+GCT	170	22.00	24.00	27.00	27.00
+GCT	171	23.00	30.00	31.00	16.00
+GCT	172	24.00	22.00	30.00	24.00
+GCT	173	24.00	17.00	33.00	26.00
+GCT	174	21.00	24.00	33.00	22.00
+GCT	175	34.00	19.00	34.00	13.00
+GCT	176	17.00	37.00	24.00	22.00
+GCT	177	24.00	24.00	25.00	27.00
+GCT	178	19.00	26.00	30.00	25.00
+GCT	179	24.00	20.00	20.00	36.00
+GCT	180	22.00	25.00	31.00	22.00
+GCT	181	21.00	17.00	38.00	24.00
+GCT	182	35.00	21.00	20.00	24.00
+GCT	183	28.00	15.00	27.00	30.00
+GCT	184	17.00	30.00	29.00	24.00
+GCT	185	16.00	32.00	33.00	19.00
+GCT	186	21.00	22.00	36.00	21.00
+GCT	187	24.00	13.00	41.00	22.00
+GCT	188	29.00	19.00	30.00	22.00
+GCT	189	19.00	23.00	33.00	25.00
+GCT	190	24.00	28.00	25.00	23.00
+GCT	191	28.00	21.00	29.00	22.00
+GCT	192	37.00	25.00	13.00	25.00
+GCT	193	18.00	26.00	25.00	31.00
+GCT	194	21.00	34.00	24.00	21.00
+GCT	195	16.00	28.00	21.00	35.00
+GCT	196	23.00	23.00	27.00	27.00
+GCT	197	18.00	20.00	24.00	38.00
+GCT	198	15.00	19.00	39.00	27.00
+GCT	199	23.00	17.00	27.00	33.00
+GCT	200	25.00	27.00	23.00	25.00
+GCT	201	26.00	19.00	25.00	30.00
+GCT	202	23.00	23.00	21.00	33.00
+GCT	203	21.00	19.00	32.00	28.00
+GCT	204	26.00	29.00	24.00	21.00
+GCT	205	16.00	23.00	21.00	40.00
+GCT	206	28.00	25.00	21.00	26.00
+GCT	207	22.00	22.00	19.00	37.00
+GCT	208	12.00	32.00	32.00	24.00
+GCT	209	18.00	20.00	15.00	47.00
+GCT	210	18.00	15.00	45.00	22.00
+GCT	211	28.00	14.00	28.00	30.00
+GCT	212	23.00	27.00	22.00	28.00
+GCT	213	22.00	12.00	34.00	32.00
+GCT	214	16.00	24.00	26.00	34.00
+GCT	215	28.00	22.00	25.00	25.00
+GCT	216	18.00	17.00	26.00	39.00
+GCT	217	27.00	30.00	16.00	27.00
+GCT	218	18.00	24.00	24.00	34.00
+GCT	219	19.00	18.00	24.00	39.00
+GCT	220	28.00	23.00	24.00	25.00
+GCT	221	20.00	24.00	20.00	36.00
+GCT	222	22.00	21.00	19.00	38.00
+GCT	223	19.00	22.00	33.00	26.00
+GCT	224	19.00	20.00	27.00	34.00
+GCT	225	14.00	32.00	34.00	20.00
+GCT	226	20.00	20.00	29.00	31.00
+GCT	227	17.00	22.00	26.00	35.00
+GCT	228	34.00	20.00	25.00	21.00
+GCT	229	22.00	27.00	16.00	35.00
+GCT	230	23.00	33.00	15.00	29.00
+GCT	231	20.00	27.00	31.00	22.00
+GCT	232	25.00	23.00	11.00	41.00
+GCT	233	22.00	25.00	27.00	26.00
+GCT	234	14.00	27.00	23.00	36.00
+GCT	235	17.00	11.00	32.00	40.00
+GCT	236	29.00	20.00	24.00	27.00
+GCT	237	16.00	19.00	23.00	42.00
+GCT	238	22.00	25.00	29.00	24.00
+GCT	239	18.00	8.00	17.00	57.00
+GCT	240	27.00	26.00	14.00	33.00
+GCT	241	21.00	22.00	17.00	40.00
+GCT	242	26.00	28.00	10.00	36.00
+GCT	243	25.00	15.00	24.00	36.00
+GCT	244	15.00	24.00	16.00	45.00
+GCT	245	24.00	23.00	19.00	34.00
+GCT	246	18.00	25.00	29.00	28.00
+GCT	247	30.00	13.00	14.00	43.00
+GCT	248	22.00	17.00	26.00	35.00
+GCT	249	25.00	22.00	22.00	31.00
+GCT	250	25.00	20.00	20.00	35.00
+GCT	251	13.00	17.00	40.00	30.00
 # ACGT content per cycle for first fragments. Use `grep ^FBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%]
 FBC	1	21.43	27.55	36.73	14.29	2.04	0.00
 FBC	2	34.00	15.00	12.00	39.00	0.00	0.00
@@ -1346,6 +1599,8 @@
 FBC	249	25.00	24.00	20.00	31.00	0.00	0.00
 FBC	250	30.00	25.00	15.00	30.00	0.00	0.00
 FBC	251	14.00	24.00	33.00	29.00	0.00	0.00
+# ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
+FTC	6178	6247	5821	6841	13
 # ACGT content per cycle for last fragments. Use `grep ^LBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%]
 LBC	1	22.45	32.65	31.63	13.27	2.04	0.00
 LBC	2	26.00	17.00	10.00	47.00	0.00	0.00
@@ -1598,6 +1853,8 @@
 LBC	249	25.00	22.00	22.00	31.00	0.00	0.00
 LBC	250	25.00	20.00	20.00	35.00	0.00	0.00
 LBC	251	13.00	17.00	40.00	30.00	0.00	0.00
+# ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
+LTC	6413	6102	5966	6606	13
 # Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs
 # Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count
 RL	251	200