annotate test-data/samtools_phase_out_3_log.txt @ 4:1e5880498f52 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
author iuc
date Tue, 28 Sep 2021 16:15:54 +0000
parents 8bfe0d1616d2
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
1 CC
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
2 CC Descriptions:
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
3 CC
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
4 CC CC comments
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
5 CC PS start of a phase set
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
6 CC FL filtered region
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
7 CC M[012] markers; 0 for singletons, 1 for phased and 2 for filtered
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
8 CC EV supporting reads; SAM format
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
9 CC // end of a phase set
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
10 CC
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
11 CC Formats of PS, FL and M[012] lines (1-based coordinates):
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
12 CC
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
13 CC PS chr phaseSetStart phaseSetEnd
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
14 CC FL chr filterStart filterEnd
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
15 CC M? chr PS pos allele0 allele1 hetIndex #supports0 #errors0 #supp1 #err1
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
16 CC
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
17 CC
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
18 PS chrI 1412 1542
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
19 M1 chrI 1412 1412 T C 1 7 0 9 0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
20 M1 chrI 1412 1414 G A 2 7 0 9 0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
21 M1 chrI 1412 1421 G A 3 7 0 9 0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
22 M1 chrI 1412 1471 T C 4 5 0 6 0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
23 M1 chrI 1412 1542 C T 5 3 0 2 0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
24 EV 0 chrI 1 40 3M * 0 0 TGG * YP:i:0 YF:i:0 YI:i:3 YO:i:0 YS:i:1366
1
8bfe0d1616d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_phase commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 0
diff changeset
25 EV 0 chrI 1 40 3M * 0 0 CAA * YP:i:1 YF:i:0 YI:i:3 YO:i:0 YS:i:1343
0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
26 EV 0 chrI 1 40 4M * 0 0 TGGT * YP:i:0 YF:i:0 YI:i:4 YO:i:0 YS:i:1409
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
27 EV 0 chrI 1 40 3M * 0 0 CAA * YP:i:1 YF:i:0 YI:i:3 YO:i:0 YS:i:1353
1
8bfe0d1616d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_phase commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 0
diff changeset
28 EV 0 chrI 1 40 3M * 0 0 TGG * YP:i:0 YF:i:0 YI:i:3 YO:i:0 YS:i:1358
8bfe0d1616d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_phase commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 0
diff changeset
29 EV 0 chrI 1 40 4M * 0 0 CAAC * YP:i:1 YF:i:0 YI:i:4 YO:i:0 YS:i:1374
0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
30 EV 0 chrI 1 40 3M * 0 0 CAA * YP:i:1 YF:i:0 YI:i:3 YO:i:0 YS:i:1350
1
8bfe0d1616d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_phase commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 0
diff changeset
31 EV 0 chrI 1 40 4M * 0 0 CAAC * YP:i:1 YF:i:0 YI:i:4 YO:i:0 YS:i:1379
0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
32 EV 0 chrI 1 40 4M * 0 0 CAAC * YP:i:1 YF:i:0 YI:i:4 YO:i:0 YS:i:1389
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
33 EV 0 chrI 1 40 3M * 0 0 TGG * YP:i:0 YF:i:0 YI:i:3 YO:i:0 YS:i:1341
1
8bfe0d1616d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_phase commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 0
diff changeset
34 EV 0 chrI 1 40 3M * 0 0 TGG * YP:i:0 YF:i:0 YI:i:3 YO:i:0 YS:i:1340
8bfe0d1616d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_phase commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 0
diff changeset
35 EV 0 chrI 1 40 3M * 0 0 CAA * YP:i:1 YF:i:0 YI:i:3 YO:i:0 YS:i:1359
0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
36 EV 0 chrI 1 40 4M * 0 0 CAAC * YP:i:1 YF:i:0 YI:i:4 YO:i:0 YS:i:1392
1
8bfe0d1616d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_phase commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 0
diff changeset
37 EV 0 chrI 1 40 4M * 0 0 TGGT * YP:i:0 YF:i:0 YI:i:4 YO:i:0 YS:i:1407
8bfe0d1616d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_phase commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 0
diff changeset
38 EV 0 chrI 1 40 3M * 0 0 TGG * YP:i:0 YF:i:0 YI:i:3 YO:i:0 YS:i:1346
8bfe0d1616d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_phase commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 0
diff changeset
39 EV 0 chrI 1 40 3M * 0 0 CAA * YP:i:1 YF:i:0 YI:i:3 YO:i:0 YS:i:1348
8bfe0d1616d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_phase commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 0
diff changeset
40 EV 0 chrI 4 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:1444
0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
41 EV 0 chrI 4 40 2M * 0 0 CT * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:1462
1
8bfe0d1616d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_phase commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 0
diff changeset
42 EV 0 chrI 4 40 2M * 0 0 CT * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:1457
0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
43 EV 0 chrI 4 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:1468
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
44 EV 0 chrI 4 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:1461
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
45 //
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
46 PS chrI 3611 3731
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
47 M1 chrI 3611 3611 T A 6 5 0 4 0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
48 M1 chrI 3611 3659 C T 7 9 0 6 0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
49 M1 chrI 3611 3731 T A 8 4 0 1 1
1
8bfe0d1616d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_phase commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 0
diff changeset
50 EV 0 chrI 6 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3569
0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
51 EV 0 chrI 6 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3569
1
8bfe0d1616d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_phase commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 0
diff changeset
52 EV 0 chrI 6 40 2M * 0 0 AT * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:3576
0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
53 EV 0 chrI 6 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3571
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
54 EV 0 chrI 6 40 2M * 0 0 AT * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:3568
1
8bfe0d1616d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_phase commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 0
diff changeset
55 EV 0 chrI 6 40 2M * 0 0 AT * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:3578
8bfe0d1616d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_phase commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 0
diff changeset
56 EV 0 chrI 6 40 2M * 0 0 AT * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:3590
8bfe0d1616d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_phase commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 0
diff changeset
57 EV 0 chrI 6 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3559
0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
58 EV 0 chrI 6 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3609
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
59 EV 0 chrI 7 40 2M * 0 0 TA * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:3644
1
8bfe0d1616d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_phase commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 0
diff changeset
60 EV 0 chrI 7 40 2M * 0 0 CT * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3651
8bfe0d1616d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_phase commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 0
diff changeset
61 EV 0 chrI 7 40 2M * 0 0 CT * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3637
8bfe0d1616d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_phase commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 0
diff changeset
62 EV 0 chrI 7 40 2M * 0 0 CT * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3647
0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
63 EV 0 chrI 7 40 2M * 0 0 TT * YP:i:1 YF:i:0 YI:i:1 YO:i:1 YS:i:3657
1
8bfe0d1616d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_phase commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 0
diff changeset
64 EV 0 chrI 7 40 2M * 0 0 CT * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3644
0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
65 //