Mercurial > repos > devteam > samtools_stats

diff test-data/12.3reads.nooverlap.expected @ 9:ab75c7ea49a5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
author iuc
date Tue, 28 Sep 2021 16:08:22 +0000
parents 8d500e0e0dbe
children 8fecc86e574a
line wrap: on
line diff
--- a/test-data/12.3reads.nooverlap.expected	Thu Oct 10 03:39:57 2019 -0400
+++ b/test-data/12.3reads.nooverlap.expected	Tue Sep 28 16:08:22 2021 +0000
@@ -1,8 +1,11 @@
+# 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 -t /tmp/tmp0r5zs075/files/1/3/0/dataset_13082855-efe1-437e-8a91-ff7d013770db.dat -p -@ 0 infile
 # CHK, Checksum	[2]Read Names	[3]Sequences	[4]Qualities
 # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)
 CHK	09f8b87f	140798ec	2b989f07
 # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
-SN	raw total sequences:	3
+SN	raw total sequences:	3	# excluding supplementary and secondary reads
 SN	filtered sequences:	0
 SN	sequences:	3
 SN	is sorted:	1
@@ -17,6 +20,7 @@
 SN	reads MQ0:	0	# mapped and MQ=0
 SN	reads QC failed:	0
 SN	non-primary alignments:	0
+SN	supplementary alignments:	0
 SN	total length:	300	# ignores clipping
 SN	total first fragment length:	100	# ignores clipping
 SN	total last fragment length:	200	# ignores clipping
@@ -355,6 +359,107 @@
 GCC	98	0.00	66.67	0.00	33.33	0.00	0.00
 GCC	99	0.00	100.00	0.00	0.00	0.00	0.00
 GCC	100	0.00	0.00	0.00	100.00	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	33.33	0.00	0.00	66.67
+GCT	2	0.00	33.33	33.33	33.33
+GCT	3	0.00	33.33	33.33	33.33
+GCT	4	33.33	66.67	0.00	0.00
+GCT	5	0.00	66.67	33.33	0.00
+GCT	6	33.33	0.00	0.00	66.67
+GCT	7	33.33	0.00	0.00	66.67
+GCT	8	0.00	33.33	33.33	33.33
+GCT	9	0.00	66.67	33.33	0.00
+GCT	10	33.33	33.33	0.00	33.33
+GCT	11	33.33	33.33	0.00	33.33
+GCT	12	0.00	33.33	33.33	33.33
+GCT	13	0.00	0.00	33.33	66.67
+GCT	14	0.00	66.67	33.33	0.00
+GCT	15	33.33	66.67	0.00	0.00
+GCT	16	33.33	0.00	0.00	66.67
+GCT	17	33.33	0.00	0.00	66.67
+GCT	18	0.00	33.33	33.33	33.33
+GCT	19	0.00	33.33	33.33	33.33
+GCT	20	0.00	66.67	33.33	0.00
+GCT	21	33.33	66.67	0.00	0.00
+GCT	22	33.33	0.00	0.00	66.67
+GCT	23	0.00	0.00	33.33	66.67
+GCT	24	0.00	33.33	33.33	33.33
+GCT	25	33.33	66.67	0.00	0.00
+GCT	26	33.33	33.33	0.00	33.33
+GCT	27	0.00	33.33	33.33	33.33
+GCT	28	0.00	33.33	33.33	33.33
+GCT	29	0.00	0.00	33.33	66.67
+GCT	30	33.33	66.67	0.00	0.00
+GCT	31	33.33	66.67	0.00	0.00
+GCT	32	33.33	0.00	0.00	66.67
+GCT	33	0.00	0.00	33.33	66.67
+GCT	34	0.00	33.33	33.33	33.33
+GCT	35	33.33	33.33	0.00	33.33
+GCT	36	0.00	66.67	33.33	0.00
+GCT	37	33.33	66.67	0.00	0.00
+GCT	38	33.33	0.00	0.00	66.67
+GCT	39	0.00	0.00	33.33	66.67
+GCT	40	0.00	33.33	33.33	33.33
+GCT	41	33.33	66.67	0.00	0.00
+GCT	42	33.33	33.33	0.00	33.33
+GCT	43	0.00	33.33	33.33	33.33
+GCT	44	0.00	33.33	33.33	33.33
+GCT	45	0.00	33.33	33.33	33.33
+GCT	46	33.33	66.67	0.00	0.00
+GCT	47	33.33	33.33	0.00	33.33
+GCT	48	33.33	0.00	0.00	66.67
+GCT	49	0.00	0.00	33.33	66.67
+GCT	50	0.00	66.67	33.33	0.00
+GCT	51	33.33	66.67	0.00	0.00
+GCT	52	0.00	66.67	33.33	0.00
+GCT	53	33.33	0.00	0.00	66.67
+GCT	54	33.33	0.00	0.00	66.67
+GCT	55	0.00	33.33	33.33	33.33
+GCT	56	0.00	66.67	33.33	0.00
+GCT	57	33.33	33.33	0.00	33.33
+GCT	58	33.33	33.33	0.00	33.33
+GCT	59	0.00	33.33	33.33	33.33
+GCT	60	0.00	0.00	33.33	66.67
+GCT	61	0.00	66.67	33.33	0.00
+GCT	62	33.33	66.67	0.00	0.00
+GCT	63	33.33	0.00	0.00	66.67
+GCT	64	33.33	0.00	0.00	66.67
+GCT	65	0.00	33.33	33.33	33.33
+GCT	66	0.00	33.33	33.33	33.33
+GCT	67	33.33	66.67	0.00	0.00
+GCT	68	0.00	66.67	33.33	0.00
+GCT	69	33.33	0.00	0.00	66.67
+GCT	70	33.33	0.00	0.00	66.67
+GCT	71	0.00	33.33	33.33	33.33
+GCT	72	0.00	66.67	33.33	0.00
+GCT	73	33.33	33.33	0.00	33.33
+GCT	74	33.33	33.33	0.00	33.33
+GCT	75	0.00	33.33	33.33	33.33
+GCT	76	0.00	0.00	33.33	66.67
+GCT	77	0.00	66.67	33.33	0.00
+GCT	78	33.33	66.67	0.00	0.00
+GCT	79	33.33	0.00	0.00	66.67
+GCT	80	33.33	0.00	0.00	66.67
+GCT	81	0.00	33.33	33.33	33.33
+GCT	82	0.00	66.67	33.33	0.00
+GCT	83	0.00	66.67	33.33	0.00
+GCT	84	33.33	33.33	0.00	33.33
+GCT	85	33.33	0.00	0.00	66.67
+GCT	86	0.00	0.00	33.33	66.67
+GCT	87	0.00	66.67	33.33	0.00
+GCT	88	33.33	66.67	0.00	0.00
+GCT	89	33.33	33.33	0.00	33.33
+GCT	90	0.00	0.00	33.33	66.67
+GCT	91	0.00	33.33	33.33	33.33
+GCT	92	0.00	66.67	33.33	0.00
+GCT	93	33.33	66.67	0.00	0.00
+GCT	94	33.33	33.33	0.00	33.33
+GCT	95	33.33	0.00	0.00	66.67
+GCT	96	0.00	33.33	33.33	33.33
+GCT	97	33.33	0.00	33.33	33.33
+GCT	98	33.33	66.67	0.00	0.00
+GCT	99	0.00	66.67	33.33	0.00
+GCT	100	33.33	0.00	0.00	66.67
 # 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	0.00	0.00	0.00	100.00	0.00	0.00
 FBC	2	0.00	100.00	0.00	0.00	0.00	0.00
@@ -456,6 +561,8 @@
 FBC	98	0.00	0.00	0.00	100.00	0.00	0.00
 FBC	99	0.00	100.00	0.00	0.00	0.00	0.00
 FBC	100	0.00	0.00	0.00	100.00	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	0	51	0	49	0
 # 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	0.00	0.00	0.00	100.00	0.00	0.00
 LBC	2	0.00	50.00	0.00	50.00	0.00	0.00
@@ -557,6 +664,26 @@
 LBC	98	0.00	100.00	0.00	0.00	0.00	0.00
 LBC	99	0.00	100.00	0.00	0.00	0.00	0.00
 LBC	100	0.00	0.00	0.00	100.00	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	1	102	0	97	0
+# ACGT content per cycle for barcodes. Use `grep ^BCC | 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 counts as a percentage of all A/C/G/T bases [%]
+BCC1	2	0.00	0.00	100.00	0.00	0.00
+BCC1	3	0.00	0.00	0.00	100.00	0.00
+BCC1	4	0.00	100.00	0.00	0.00	0.00
+BCC1	5	0.00	0.00	0.00	100.00	0.00
+BCC1	6	100.00	0.00	0.00	0.00	0.00
+BCC1	7	0.00	0.00	0.00	100.00	0.00
+BCC1	8	0.00	100.00	0.00	0.00	0.00
+# Barcode Qualities. Use `grep ^QTQ | cut -f 2-` to extract this part.
+# Columns correspond to qualities and rows to barcode cycles. First column is the cycle number.
+QTQ1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+QTQ1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+QTQ1	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
+QTQ1	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0
+QTQ1	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1
+QTQ1	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1
+QTQ1	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1
+QTQ1	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0
 # 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
 IS	0	0	0	0	0
 IS	1	0	0	0	0