Mercurial > repos > devteam > samtools_stats

diff test-data/12.2reads.nooverlap.expected @ 8:e28839a4b932 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 16:17:39 +0000
parents 95a7ddf617e7
children 541082d03bef
line wrap: on
line diff
--- a/test-data/12.2reads.nooverlap.expected	Thu Oct 17 02:21:23 2019 -0400
+++ b/test-data/12.2reads.nooverlap.expected	Tue Sep 28 16:17:39 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/b/2/1/dataset_b2175431-044e-449d-8f60-1bfd33679b61.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	5b31676a	b0edee94	471895da
 # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
-SN	raw total sequences:	2
+SN	raw total sequences:	2	# excluding supplementary and secondary reads
 SN	filtered sequences:	0
 SN	sequences:	2
 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:	200	# ignores clipping
 SN	total first fragment length:	100	# ignores clipping
 SN	total last fragment length:	100	# ignores clipping
@@ -353,6 +357,107 @@
 GCC	98	50.00	50.00	0.00	0.00	0.00	0.00
 GCC	99	50.00	50.00	0.00	0.00	0.00	0.00
 GCC	100	100.00	0.00	0.00	0.00	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	50.00	0.00	50.00	0.00
+GCT	2	0.00	50.00	50.00	0.00
+GCT	3	0.00	50.00	0.00	50.00
+GCT	4	0.00	50.00	50.00	0.00
+GCT	5	0.00	0.00	50.00	50.00
+GCT	6	0.00	0.00	50.00	50.00
+GCT	7	0.00	50.00	0.00	50.00
+GCT	8	0.00	0.00	50.00	50.00
+GCT	9	0.00	50.00	0.00	50.00
+GCT	10	50.00	0.00	50.00	0.00
+GCT	11	0.00	0.00	100.00	0.00
+GCT	12	50.00	0.00	0.00	50.00
+GCT	13	0.00	50.00	50.00	0.00
+GCT	14	50.00	0.00	0.00	50.00
+GCT	15	0.00	0.00	50.00	50.00
+GCT	16	0.00	50.00	50.00	0.00
+GCT	17	0.00	50.00	0.00	50.00
+GCT	18	100.00	0.00	0.00	0.00
+GCT	19	50.00	0.00	0.00	50.00
+GCT	20	0.00	50.00	50.00	0.00
+GCT	21	50.00	0.00	0.00	50.00
+GCT	22	0.00	50.00	0.00	50.00
+GCT	23	0.00	0.00	0.00	100.00
+GCT	24	0.00	50.00	50.00	0.00
+GCT	25	0.00	0.00	0.00	100.00
+GCT	26	0.00	0.00	50.00	50.00
+GCT	27	0.00	100.00	0.00	0.00
+GCT	28	0.00	0.00	0.00	100.00
+GCT	29	50.00	0.00	50.00	0.00
+GCT	30	0.00	50.00	0.00	50.00
+GCT	31	0.00	50.00	0.00	50.00
+GCT	32	0.00	0.00	50.00	50.00
+GCT	33	0.00	50.00	0.00	50.00
+GCT	34	50.00	0.00	0.00	50.00
+GCT	35	0.00	50.00	0.00	50.00
+GCT	36	0.00	100.00	0.00	0.00
+GCT	37	0.00	50.00	0.00	50.00
+GCT	38	50.00	50.00	0.00	0.00
+GCT	39	100.00	0.00	0.00	0.00
+GCT	40	0.00	0.00	100.00	0.00
+GCT	41	0.00	50.00	0.00	50.00
+GCT	42	50.00	50.00	0.00	0.00
+GCT	43	0.00	0.00	50.00	50.00
+GCT	44	50.00	0.00	50.00	0.00
+GCT	45	50.00	0.00	50.00	0.00
+GCT	46	50.00	0.00	50.00	0.00
+GCT	47	50.00	0.00	50.00	0.00
+GCT	48	0.00	50.00	50.00	0.00
+GCT	49	50.00	0.00	0.00	50.00
+GCT	50	0.00	0.00	50.00	50.00
+GCT	51	0.00	0.00	100.00	0.00
+GCT	52	50.00	0.00	50.00	0.00
+GCT	53	0.00	50.00	0.00	50.00
+GCT	54	50.00	0.00	50.00	0.00
+GCT	55	50.00	0.00	0.00	50.00
+GCT	56	0.00	50.00	50.00	0.00
+GCT	57	100.00	0.00	0.00	0.00
+GCT	58	50.00	0.00	50.00	0.00
+GCT	59	100.00	0.00	0.00	0.00
+GCT	60	50.00	0.00	50.00	0.00
+GCT	61	0.00	0.00	0.00	100.00
+GCT	62	0.00	50.00	50.00	0.00
+GCT	63	50.00	0.00	0.00	50.00
+GCT	64	0.00	0.00	100.00	0.00
+GCT	65	50.00	50.00	0.00	0.00
+GCT	66	0.00	50.00	0.00	50.00
+GCT	67	0.00	0.00	0.00	100.00
+GCT	68	0.00	50.00	0.00	50.00
+GCT	69	0.00	50.00	0.00	50.00
+GCT	70	50.00	0.00	0.00	50.00
+GCT	71	0.00	0.00	0.00	100.00
+GCT	72	0.00	50.00	0.00	50.00
+GCT	73	0.00	0.00	0.00	100.00
+GCT	74	0.00	50.00	0.00	50.00
+GCT	75	50.00	0.00	0.00	50.00
+GCT	76	0.00	50.00	0.00	50.00
+GCT	77	50.00	0.00	0.00	50.00
+GCT	78	50.00	0.00	0.00	50.00
+GCT	79	50.00	0.00	0.00	50.00
+GCT	80	50.00	0.00	0.00	50.00
+GCT	81	50.00	0.00	0.00	50.00
+GCT	82	50.00	0.00	0.00	50.00
+GCT	83	50.00	0.00	0.00	50.00
+GCT	84	50.00	0.00	0.00	50.00
+GCT	85	50.00	0.00	0.00	50.00
+GCT	86	50.00	0.00	0.00	50.00
+GCT	87	50.00	0.00	0.00	50.00
+GCT	88	50.00	0.00	0.00	50.00
+GCT	89	50.00	0.00	0.00	50.00
+GCT	90	50.00	0.00	0.00	50.00
+GCT	91	50.00	0.00	50.00	0.00
+GCT	92	50.00	0.00	50.00	0.00
+GCT	93	50.00	0.00	50.00	0.00
+GCT	94	50.00	0.00	0.00	50.00
+GCT	95	50.00	0.00	50.00	0.00
+GCT	96	50.00	0.00	50.00	0.00
+GCT	97	50.00	0.00	50.00	0.00
+GCT	98	50.00	0.00	50.00	0.00
+GCT	99	50.00	0.00	50.00	0.00
+GCT	100	50.00	0.00	0.00	50.00
 # 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	0.00	0.00	0.00	100.00	0.00	0.00
 FBC	2	0.00	0.00	100.00	0.00	0.00	0.00
@@ -454,6 +559,8 @@
 FBC	98	0.00	100.00	0.00	0.00	0.00	0.00
 FBC	99	0.00	100.00	0.00	0.00	0.00	0.00
 FBC	100	100.00	0.00	0.00	0.00	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	50	21	14	15	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	100.00	0.00	0.00	0.00
 LBC	2	0.00	0.00	100.00	0.00	0.00	0.00
@@ -555,6 +662,26 @@
 LBC	98	100.00	0.00	0.00	0.00	0.00	0.00
 LBC	99	100.00	0.00	0.00	0.00	0.00	0.00
 LBC	100	100.00	0.00	0.00	0.00	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	41	20	23	16	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	1	0	0
+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