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##assembly lines are lost #55

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ernfrid opened this issue Mar 10, 2016 · 1 comment
Closed

##assembly lines are lost #55

ernfrid opened this issue Mar 10, 2016 · 1 comment

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@ernfrid
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ernfrid commented Mar 10, 2016

Lines in the VCF header like ##assembly are getting scrubbed. Possibly additional lines would be scrubbed as well. Is this the proper behavior or does it need to be fixed? Seems improper to me.
@cc2qe
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cc2qe commented Mar 10, 2016

improper behavior, should be fixed

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On Mar 9, 2016, at 22:31, Dave Larson notifications@github.com wrote:

Lines in the VCF header like ##assembly are getting scrubbed. Possibly
additional lines would be scrubbed as well. Is this the proper behavior or
does it need to be fixed? Seems improper to me.

—
Reply to this email directly or view it on GitHub
#55.

ernfrid added a commit that referenced this issue Mar 30, 2016
@ernfrid
Merge pull request #69 from ernfrid/vcf_header_fixes
a8f7d0e 
Improve VCF header handling. This fixes #67 and fixes #55
ernfrid added a commit to ernfrid/svtools that referenced this issue Aug 30, 2017
@ernfrid
Squashed 'svtools/bin/svtyper/' changes from 0277531..635b8f6
6e69c85 
635b8f6 whitespace
db4b156 bump version
1309c24 change max_reads to unlimited by default
6756a0a pass max_reads as a command line argument
3849f64 Merge pull request hall-lab#56 from brentp/limit-reads
fbf9094 bump version
8193662 default behavior clears existing QUAL scores (-q flag to iterate)
609e0bf limit number of reads in gather_reads
25573aa add command line argument to clear existing QUAL field
0ed7ea9 change reference fasta flag to -T, for consistency with htslib tools
5c3a558 argument for optional reference FASTA when reading CRAM files
8637bc3 throw error if SVTYPE missing hall-lab#55

git-subtree-dir: svtools/bin/svtyper
git-subtree-split: 635b8f6e8b17345a1905963877b597110c6906e7
ernfrid added a commit to ernfrid/svtools that referenced this issue Aug 30, 2017
@ernfrid
Squashed 'svtools/bin/svtyper/' changes from 0277531..635b8f6
9502284 
635b8f6 whitespace
db4b156 bump version
1309c24 change max_reads to unlimited by default
6756a0a pass max_reads as a command line argument
3849f64 Merge pull request hall-lab#56 from brentp/limit-reads
fbf9094 bump version
8193662 default behavior clears existing QUAL scores (-q flag to iterate)
609e0bf limit number of reads in gather_reads
25573aa add command line argument to clear existing QUAL field
0ed7ea9 change reference fasta flag to -T, for consistency with htslib tools
5c3a558 argument for optional reference FASTA when reading CRAM files
8637bc3 throw error if SVTYPE missing hall-lab#55

git-subtree-dir: svtools/bin/svtyper
git-subtree-split: 635b8f6e8b17345a1905963877b597110c6906e7
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@ernfrid @cc2qe