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Commits on Feb 12, 2024

• update Changes for release 0.39.0

  dozy

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  6345633

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• Merge pull request #335 from wtsi-npg/devel

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Commits on Jan 26, 2024

• Merge branch 'devel' of github.com:wtsi-npg/p4

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Commits on Jan 25, 2024

• Merge pull request #332 from dozy/bam_cram_index_creation_changes

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Commits on Dec 4, 2023

• release 0.38.0

  dozy

  committed
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• Merge pull request #333 from wtsi-npg/devel

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Commits on Nov 22, 2023

• use "samtools index" instead of "cram_index to create cram indexes

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  dozy

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Commits on Oct 25, 2023

• Merge pull request #328 from ces/BGE1

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  dozy

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• use modern p4

  ces

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Commits on Oct 19, 2023

• add additional autosome specific coverage threshold to final_output_prep.json

  ces

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Commits on Sep 18, 2023

• update Changes for release 0.37.2

  dozy

  committed
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• Merge pull request #326 from wtsi-npg/devel

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  dozy

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Commits on Sep 7, 2023

• Merge pull request #325 from dozy/bambi_i2b_flag_tweak

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Commits on Aug 31, 2023

• change bambi i2b command in stage1 analysis to use new boolean version of --nocall-quality flag

  dozy

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Commits on Aug 15, 2023

• update Changes for release 0.37.1

  dozy

  committed
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• Merge pull request #324 from wtsi-npg/devel

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  dozy

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• Merge pull request #323 from dozy/mdm_duplexseq_mod

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Commits on Aug 10, 2023

• amend markdup_duplexseq (nanoseq) method to use:

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Commits on Aug 8, 2023

• Merge pull request #300 from jidur/merge_aligned_samtools

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• Merge branch 'devel' into merge_aligned_samtools

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Commits on Jul 25, 2023

• udate Changes for release 0.37.0

  dozy

  committed
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• Merge pull request #322 from wtsi-npg/devel

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Commits on Jul 7, 2023

• Merge pull request #321 from dozy/i2b_nocall_qual_switch

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• add i2b_nocall_qual_switch to control the i2b_nocall_qual_flag. Change default to off.

  dozy

  committed
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Commits on Jul 6, 2023

• Merge pull request #320 from dozy/i2b_nocall_qual

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Commits on Jul 3, 2023

• add --nocall-quality flag (with default value 2) to bambi i2b command

  dozy

  committed
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Commits on Jun 8, 2023

• update Changes for release 0.36.0

  dozy

  committed
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• Merge pull request #319 from wtsi-npg/devel

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Commits on Jun 6, 2023

• Merge pull request #317 from dozy/bwa_mem2_hs_fix

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• Merge pull request #318 from dozy/bbb_opt_dist_fix

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Commits on Jun 5, 2023

• add optminpixeldif flag (optical distance for duplicates) to

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  dozy

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• update Changes

  dozy

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Commits on Jun 2, 2023

• if a value is supplied for the parameter hs_bwa_executable, use that for

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  dozy

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Commits on Apr 3, 2023

• update Changes for release 0.35.0

  dozy

  committed
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• Merge pull request #316 from wtsi-npg/devel

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