diff test-data/11.stats.expected @ 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/11.stats.expected	Thu Oct 17 02:21:23 2019 -0400
+++ b/test-data/11.stats.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 -@ 0 infile ref1:10-24 ref1:30-46 ref1:39-56
 # CHK, Checksum	[2]Read Names	[3]Sequences	[4]Qualities
 # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)
 CHK	cb2d2d82	bcd83869	62ec814e
 # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
-SN	raw total sequences:	26
+SN	raw total sequences:	26	# excluding supplementary and secondary reads
 SN	filtered sequences:	0
 SN	sequences:	26
 SN	is sorted:	1
@@ -17,6 +20,7 @@
 SN	reads MQ0:	1	# mapped and MQ=0
 SN	reads QC failed:	0
 SN	non-primary alignments:	0
+SN	supplementary alignments:	0
 SN	total length:	260	# ignores clipping
 SN	total first fragment length:	140	# ignores clipping
 SN	total last fragment length:	120	# ignores clipping
@@ -89,6 +93,17 @@
 GCC	8	26.92	23.08	38.46	11.54	0.00	0.00
 GCC	9	23.08	26.92	26.92	23.08	0.00	0.00
 GCC	10	23.08	23.08	38.46	15.38	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	26.92	26.92	30.77	15.38
+GCT	2	7.69	38.46	26.92	26.92
+GCT	3	26.92	26.92	30.77	15.38
+GCT	4	11.54	34.62	26.92	26.92
+GCT	5	23.08	26.92	38.46	11.54
+GCT	6	11.54	34.62	23.08	30.77
+GCT	7	19.23	23.08	38.46	19.23
+GCT	8	11.54	38.46	23.08	26.92
+GCT	9	23.08	19.23	34.62	23.08
+GCT	10	11.54	34.62	26.92	26.92
 # 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	42.86	21.43	14.29	0.00	0.00
 FBC	2	7.14	28.57	42.86	21.43	0.00	0.00
@@ -100,6 +115,8 @@
 FBC	8	21.43	28.57	28.57	21.43	0.00	0.00
 FBC	9	21.43	21.43	35.71	21.43	0.00	0.00
 FBC	10	14.29	28.57	35.71	21.43	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	24	43	45	28	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	16.67	41.67	8.33	33.33	0.00	0.00
 LBC	2	33.33	8.33	50.00	8.33	0.00	0.00
@@ -111,6 +128,19 @@
 LBC	8	33.33	16.67	50.00	0.00	0.00	0.00
 LBC	9	25.00	33.33	16.67	25.00	0.00	0.00
 LBC	10	33.33	16.67	41.67	8.33	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	30	33	36	21	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	1	50.00	0.00	0.00	50.00	0.00
+BCC1	2	0.00	50.00	50.00	0.00	0.00
+BCC1	3	0.00	50.00	50.00	0.00	0.00
+BCC1	4	50.00	0.00	0.00	50.00	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
+QTQ1	2
+QTQ1	3
+QTQ1	4
 # 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