details: http://www.bx.psu.edu/hg/galaxy/rev/1dc7e6c15272
changeset: 3659:1dc7e6c15272
user: Dan Blankenberg <dan(a)bx.psu.edu>
date: Thu Apr 15 12:33:28 2010 -0400
description:
Have fastq set_meta() only skip counting 'comment lines' when they are before any sequences. This is still not properly determining sequence counts in cases where line wrapping occurs; quality score lines can start with e.g. '#' and '@'.
diffstat:
lib/galaxy/datatypes/sequence.py | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
diffs (12 lines):
diff -r df40eae8e86b -r 1dc7e6c15272 lib/galaxy/datatypes/sequence.py
--- a/lib/galaxy/datatypes/sequence.py Thu Apr 15 11:10:57 2010 -0400
+++ b/lib/galaxy/datatypes/sequence.py Thu Apr 15 12:33:28 2010 -0400
@@ -163,7 +163,7 @@
seq_counter = 0 # blocks should be 4 lines long
for line in file( dataset.file_name ):
line = line.strip()
- if line and line.startswith( '#' ):
+ if line and line.startswith( '#' ) and not sequences:
# We don't count comment lines for sequence data types
continue
if line and line.startswith( '@' ):
details: http://www.bx.psu.edu/hg/galaxy/rev/df40eae8e86b
changeset: 3658:df40eae8e86b
user: Anton Nekrutenko <anton(a)bx.psu.edu>
date: Thu Apr 15 11:10:57 2010 -0400
description:
changes to help text
diffstat:
tools/samtools/pileup_parser.xml | 10 +++++-----
1 files changed, 5 insertions(+), 5 deletions(-)
diffs (48 lines):
diff -r 33eab99a2df5 -r df40eae8e86b tools/samtools/pileup_parser.xml
--- a/tools/samtools/pileup_parser.xml Thu Apr 15 10:51:51 2010 -0400
+++ b/tools/samtools/pileup_parser.xml Thu Apr 15 11:10:57 2010 -0400
@@ -93,7 +93,7 @@
<param name="type_select" value="ten"/>
<param name="qv_cutoff" value="20" />
<param name="cvrg_cutoff" value="3" />
- <param name="snps_only" value="Yes"/>
+ <param name="snps_only" value="Yes"/>q
<param name="interval" value="Yes" />
<param name="diff" value="No" />
<param name="qc_base" value="Yes" />
@@ -183,7 +183,7 @@
2 Position (1-based)
3 Reference base at that position
4 Coverage (# reads aligning over that position)
- 5 Bases within reads where (see Galaxy wiki for more info)
+ 5 Bases within reads
6 Quality values (phred33 scale, see Galaxy wiki for more)
**Ten column pileup**
@@ -210,7 +210,7 @@
6 SNP quality
7 Maximum mapping quality
8 Coverage (# reads aligning over that position)
- 9 Bases within reads where (see Galaxy wiki for more info)
+ 9 Bases within reads
10 Quality values (phred33 scale, see Galaxy wiki for more)
@@ -255,7 +255,7 @@
2 Position (1-based)
3 Reference base at that position
4 Coverage (# reads aligning over that position)
- 5 Bases within reads where (see Galaxy wiki for more info)
+ 5 Bases within reads where
6 Quality values (phred33 scale, see Galaxy wiki for more)
7 Number of A variants
8 Number of C variants
@@ -289,7 +289,7 @@
3 End position (1-based)
4 Reference base at that position
5 Coverage (# reads aligning over that position)
- 6 Bases within reads where (see Galaxy wiki for more info)
+ 6 Bases within reads
7 Quality values (phred33 scale, see Galaxy wiki for more)
8 Number of A variants
9 Number of C variants