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Commits on Sep 8, 2021

• Allow index -s on index file only w/o data file present

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Commits on Jul 4, 2021

• Include <strings.h> directly where needed [minor]

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  jmarshall

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Commits on Jun 29, 2021

• Accept index file names as well as data file names

  pd3

  committed
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Commits on Jun 17, 2021

• Use bcf_hdr_id2name directly, instead of bcf_index_seqnames.

  valeriuo

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• Try to work just with the index file when calculating record statistics.

  valeriuo

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Commits on Feb 16, 2020

• Rename the option --output-file to --output to make it consistent across bcftools commands.

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  pd3

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Commits on Jul 21, 2019

• Clarify the meaning of the --threads option.

  pd3

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Commits on Jul 19, 2018

• Check return status of all *write() and *close() calls

  pd3

  committed
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Commits on Mar 22, 2018

• The indexed file must be BGZF-compressed. Resolves samtools#761

  pd3

  committed
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Commits on Sep 14, 2017

• Truncated files can be indexed only with the -f option. Resolved samtools#659

  pd3

  committed
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Commits on Mar 8, 2017

• update some missing documentation

  mcshane

  committed
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Commits on Feb 23, 2017

• index: update error message for failure to index

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  mcshane

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Commits on Nov 1, 2016

• Added multi-threading for reads on annotate, index, merge, roh and view.

  

  jkbonfield

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  pd3

  committed
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Commits on Aug 2, 2016

• index: add option to set the path for the index file (samtools#437)

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  mcshane

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Commits on Jan 11, 2016

• index: do not segfault when indexing non-existent files. Fixes samtools#367

  

  pd3

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  mcshane

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Commits on Sep 30, 2015

• vcfindex: make index -s work even if length attribute is not present

  

  pd3

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  mcshane

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Commits on Jan 16, 2015

• Replaced ato[if] with strto[lf] to recognise user errors

  pd3

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Commits on Nov 3, 2014

• Use hts_get_format() rather than direct access to htsFile internals

  jmarshall

  committed
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Commits on Oct 20, 2014

• use new htslib file type detection and error reporting API

  pd3

  committed
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Commits on Aug 29, 2014

• update index stats option to output contig lengths too

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Commits on Aug 28, 2014

• new options to print stats based on the index files

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Commits on Aug 14, 2014

• Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT

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  jmarshall

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Commits on Aug 13, 2014

• Reformat license text

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  jmarshall

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Commits on Aug 11, 2014

• Write out description and author in each source file header

  jmarshall

  committed
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Commits on Jul 10, 2014

• vcfindex: add shortcut options for TBI and CSI index creation

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  mcshane

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Commits on May 21, 2014

• index: Minor change of error message

  pd3

  committed
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Commits on Feb 18, 2014

• index: Do not require -f if data file newer than index file

  pd3

  committed
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Commits on Feb 7, 2014

• bcftools index now works on vcf and bcf; defaults to .csi

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