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Commits on Oct 16, 2019

• Support for simple fill-tags expressions such as "-t DP=sum(DP)"

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Commits on Oct 10, 2019

• Add new -N, --replace-non-ACGTN option. Resolves samtools#1088

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Commits on Sep 26, 2019

• Better handling of plugin arguments.

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Commits on Sep 25, 2019

• Merge branch 'develop' of github.com:samtools/bcftools into develop

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• Add --single-overlaps option to invoke the pre-af6f0c9 behavior. Resolves samtools#1047 (comment)

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• More 64 bit preparations

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• Numeric types can use --merge-logic append as well. This adds to samtools#1047

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• Merge pull request samtools#1083 from daviesrob/bigness

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• Print stderr of failed tests, otherwise it can be difficult to guess why travis fails

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Commits on Sep 23, 2019

• Clean up a minor memory leak

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• Merge branch 'develop' of github.com:samtools/bcftools into develop

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• New mpileup -a SCR annotation which gives the number of soft-clipped reads

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Commits on Sep 20, 2019

• Make the annotate -x FILTER/x command exit gracefully.

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• Fix minor bug

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• Merge pull request samtools#1086 from jmarshall/dependencies

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• Check that a filename has been provided [minor]

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• Fix Makefile dependencies

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Commits on Sep 17, 2019

• Merge branch 'develop' of github.com:samtools/bcftools into develop

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• Check if the input file is sorted, otherwise errors might be thrown with a cryptic message ("this should not happen")

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Commits on Sep 14, 2019

• Resolve possible sample name conflicts with merging. Fixes samtools#1081

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• Fix bug in gVCF merging. Hopefully this fixes samtools#1080

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Commits on Sep 9, 2019

• Prepare for 64-bit positions

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Commits on Aug 30, 2019

• Merge pull request samtools#1075 from pvanheus/patch-1

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• use /usr/bin/env perl

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Commits on Aug 20, 2019

• Make split-vep -A work even for variable number of CSQ fields

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• Minor: add a forgotten switch to the usage text

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Commits on Aug 15, 2019

• Make the -i/-e function COUNT() with INFO tags as well. Resolves samtools#1069

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Commits on Aug 12, 2019

• Complain if the check of reference was requested but the reference was not given

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Commits on Aug 10, 2019

• Add filtering support for within-sample comparison of FORMAT fields. Resolves samtools#1063

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Commits on Aug 7, 2019

• Fix Windows build.

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Commits on Aug 3, 2019

• Extend annotate -l to work with numeric types.

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Commits on Aug 2, 2019

• Fix segfault on missing ALT allele and add --no-version option. Resolves samtools#1061

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Commits on Aug 1, 2019

• Merge pull request samtools#1057 from jmarshall/diagnostics

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Commits on Jul 31, 2019

• Avoid non-portable uname -o option and only invoke uname once

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  jmarshall

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• Add vcfsort error message; suppress various compiler warnings

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