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Replace '\t' to ' ' in BAM headers

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This commit is contained in:
ashvark
2017-07-10 11:26:34 +02:00
parent 0cfdfbf275
commit 90a0ab0398
1 changed files with 3 additions and 3 deletions
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lib/galaxy/datatypes/binary.py
+3 -3
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@@ -474,7 +474,7 @@ class Bam( Binary ):
ck_data = ""
header_line_count = 0
if offset == 0:
ck_data = bamfile.text
ck_data = bamfile.text.replace('\t',' ')
header_line_count = bamfile.text.count('\n')
else:
bamfile.seek( offset )
@@ -486,9 +486,9 @@ class Bam( Binary ):
break
else:
bamline = alignment.tostring( bamfile )
# Galaxy display each tag as separate column because 'tostring()' funcition put spaces in between each tag of tags column.
# Galaxy display each tag as separate column because 'tostring()' funcition put tabs in between each tag of tags column.
# Below code will remove spaces between each tag.
bamline_modified = ('\t').join( bamline.split()[:11] + [ ('').join(bamline.split()[11:]) ] )
bamline_modified = ('\t').join( bamline.split()[:11] + [ (' ').join(bamline.split()[11:]) ] )
ck_data = "%s\n%s" % ( ck_data, bamline_modified )
return dumps( { 'ck_data': util.unicodify( ck_data ),
'offset': offset } )