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tabix -H does not work for VCF #249

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mktrost opened this issue Aug 5, 2015 · 1 comment
Closed

tabix -H does not work for VCF #249

mktrost opened this issue Aug 5, 2015 · 1 comment

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@mktrost
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mktrost commented Aug 5, 2015

Tabix help says:
-H, --only-header print only the header lines
But when I try running with that option on a vcf, it returns nothing. If I use an old version of tabix, I get the VCF header.
mcshane added a commit that referenced this issue Aug 5, 2015
@mcshane
tabix: fixes --only-header option so that is now works!
48801dd 
Fixes #249
@mcshane mcshane mentioned this issue Aug 5, 2015
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mcshane added a commit that referenced this issue Aug 5, 2015
@mcshane @jmarshall
tabix: fixes --only-header option so that it now works!
4c82a74 
Fixes #249

[NEWS]
* tabix --only-header works again (was broken in 1.2.x; #249)
@jmarshall
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This worked in 1.1, but was broken in 1.2 and 1.2.1 by a ed3efe9 thinko.

charles-plessy added a commit to Debian/htslib that referenced this issue Dec 24, 2015
@charles-plessy
Merge tag '1.3' into debian/unstable
68e6f6c 
HTSlib release 1.3, plugins, libcurl, CRAM v3.0, bug fixes

* Files can now be accessed via HTTPS and Amazon S3 in addition to HTTP
  and FTP, when HTSlib is configured to use libcurl for network file access
  rather than the included basic knetfile networking.

* HTSlib can be built to use remote access hFILE backends (such as iRODS
  and libcurl) via a plugin mechanism.  This allows other backends to be
  easily added and facilitates building tools that use HTSlib, as they
  don't need to be linked with the backends' various required libraries.

* fai_build() and samtools faidx now accept initial whitespace in ">"
  headers (e.g., "> chr1 description" is taken to refer to "chr1").

* tabix --only-header works again (was broken in 1.2.x; samtools#249).

* HTSlib's configure script and Makefile now fully support the standard
  convention of allowing CC/CPPFLAGS/CFLAGS/LDFLAGS/LIBS to be overridden
  as needed.  Previously the Makefile listened to $(LDLIBS) instead; if you
  were overriding that, you should now override LIBS rather than LDLIBS.

* Fixed bugs samtools#168, samtools#172, samtools#176, samtools#197, samtools#206, samtools#225, samtools#245, samtools#265, samtools#295, and samtools#296.
pd3 pushed a commit to pd3/htslib that referenced this issue May 4, 2018
@magicDGS @jmarshall
Add Read Group header optional BC tag field (PR samtools#250)
5b84bd3 
Fixes samtools#249, which proposed adding this field.
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@jmarshall @mktrost