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Commits on Jul 20, 2020

• [stats] Add new GCT section to stats (PR #1274)

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  valeriuo

  authored
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• Add an options to specifiy index location. (PR #1283)

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  whitwham

  authored
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Commits on Jul 9, 2020

• Reformat NEWS entry after wording change [trivial]

  jmarshall

  committed
  ba462f6

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• Restore mpileup --output-MQ --output-BP column ordering

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  jmarshall

  authored and

  valeriuo

  committed
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Commits on Jul 7, 2020

• Delete MD and NM tags unless asked not to.

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  whitwham

  authored and

  daviesrob

  committed
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• Option to add OA tags.

  

  whitwham

  authored and

  daviesrob

  committed
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• Fix samtools coverage help message and quality option usage. (PR #1279)

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  valeriuo

  authored
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Commits on Jun 30, 2020

• Allow "tview -w INT" to work on html too.

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  jkbonfield

  committed
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Commits on Jun 29, 2020

• Add -w option to allow wider window with -d T

  pd3

  committed
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Commits on Jun 24, 2020

• Rebase, refactor, increase the base quality threshold to 1.

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  valeriuo

  committed
  3156bea

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• Add bam_mplp_init_overlaps func to insure an overlap pair reads should be

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  TuBieJun

  authored and

  valeriuo

  committed
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Commits on Jun 23, 2020

• Add -u option to various samtools commands. (PR #1265)

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  jkbonfield

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Commits on Jun 17, 2020

• Added VDEPTH section.

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  jkbonfield

  authored and

  valeriuo

  committed
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• Added two new output types to ampliconstats / plot.

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  jkbonfield

  authored and

  valeriuo

  committed
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• Plot-ampliconstats improvements

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  jkbonfield

  authored and

  valeriuo

  committed
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• Samtools ampliconstats updates.

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  jkbonfield

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  valeriuo

  committed
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Commits on Jun 2, 2020

• Typo fixes [minor]

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  jmarshall

  committed
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Commits on May 22, 2020

• Allow depth to display 0 coverage on files with no reads.

  valeriuo

  committed
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Commits on May 19, 2020

• Prevent a couple of buffer overflows that might occur when the amplicon

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  valeriuo

  authored and

  jkbonfield

  committed
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• Merge more ampliconstats improvements (PR #1236)

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  daviesrob

  committed
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Commits on May 14, 2020

• Added tests and tweaked documentation.

  

  whitwham

  authored and

  daviesrob

  committed
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• Add filter and fail marking options.

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  whitwham

  authored and

  daviesrob

  committed
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• Mention BAI chromosome length limit in samtools index man page (PR #1248)

  jmarshall

  authored
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Commits on May 13, 2020

• Allow bedcov to read space separated BED files.

  valeriuo

  committed
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• Fix > vs >= in samtools depth man page.

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  jkbonfield

  committed
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• Fixes TODO in previous commit.

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  jkbonfield

  committed
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• Autoscale read count/depth plots.

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  jkbonfield

  committed
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• Improvements to ampliconstats help message.

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  mcshane

  authored and

  jkbonfield

  committed
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Commits on May 12, 2020

• Added simple ampliconstats test.

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  jkbonfield

  committed
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• Improve ampliconstats when dealing with single-ended data.

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  jkbonfield

  committed
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• Improved robustness of plot-ampliconstats.

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  jkbonfield

  committed
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• Added FTCOORD/CTCOORD ampliconstats plots.

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  jkbonfield

  committed
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• Reorder ampliconstats output.

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  jkbonfield

  committed
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• Change ampliconstats TLEN to TCOORD.

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  jkbonfield

  committed
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• Ampliconstats improvements.

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  jkbonfield

  committed
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