diff test-data/2.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/2.stats.expected	Thu Oct 17 02:21:23 2019 -0400
+++ b/test-data/2.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 --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	1a1c1362	29c426ae	7bab45da
 # 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:	70	# ignores clipping
 SN	total first fragment length:	35	# ignores clipping
 SN	total last fragment length:	35	# ignores clipping
@@ -195,6 +199,42 @@
 GCC	33	50.00	0.00	0.00	50.00	0.00	0.00
 GCC	34	50.00	0.00	50.00	0.00	0.00	0.00
 GCC	35	0.00	0.00	50.00	50.00	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	0.00	50.00	0.00	50.00
+GCT	2	50.00	0.00	50.00	0.00
+GCT	3	0.00	0.00	50.00	50.00
+GCT	4	0.00	0.00	100.00	0.00
+GCT	5	0.00	0.00	50.00	50.00
+GCT	6	0.00	50.00	0.00	50.00
+GCT	7	0.00	0.00	50.00	50.00
+GCT	8	0.00	0.00	0.00	100.00
+GCT	9	0.00	50.00	50.00	0.00
+GCT	10	50.00	0.00	50.00	0.00
+GCT	11	50.00	0.00	0.00	50.00
+GCT	12	50.00	0.00	50.00	0.00
+GCT	13	50.00	0.00	50.00	0.00
+GCT	14	0.00	0.00	0.00	100.00
+GCT	15	100.00	0.00	0.00	0.00
+GCT	16	50.00	0.00	0.00	50.00
+GCT	17	0.00	0.00	50.00	50.00
+GCT	18	0.00	50.00	50.00	0.00
+GCT	19	0.00	100.00	0.00	0.00
+GCT	20	0.00	0.00	50.00	50.00
+GCT	21	0.00	0.00	100.00	0.00
+GCT	22	0.00	50.00	0.00	50.00
+GCT	23	50.00	0.00	0.00	50.00
+GCT	24	50.00	0.00	50.00	0.00
+GCT	25	50.00	0.00	50.00	0.00
+GCT	26	0.00	0.00	100.00	0.00
+GCT	27	50.00	0.00	0.00	50.00
+GCT	28	0.00	0.00	50.00	50.00
+GCT	29	0.00	50.00	0.00	50.00
+GCT	30	0.00	50.00	0.00	50.00
+GCT	31	0.00	50.00	50.00	0.00
+GCT	32	0.00	0.00	100.00	0.00
+GCT	33	100.00	0.00	0.00	0.00
+GCT	34	0.00	0.00	50.00	50.00
+GCT	35	50.00	0.00	50.00	0.00
 # 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
@@ -231,6 +271,8 @@
 FBC	33	100.00	0.00	0.00	0.00	0.00	0.00
 FBC	34	0.00	0.00	100.00	0.00	0.00	0.00
 FBC	35	0.00	0.00	100.00	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	6	5	15	9	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	0.00	100.00	0.00	0.00
@@ -267,6 +309,8 @@
 LBC	33	0.00	0.00	0.00	100.00	0.00	0.00
 LBC	34	100.00	0.00	0.00	0.00	0.00	0.00
 LBC	35	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	11	10	5	9	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