Code

Max buffer size argument for uniq#201

Code

Merged

andrewdavidsmith merged 23 commits intomastersmithlabcode/dnmtools:masterfrom uniq-max-buffer-sizesmithlabcode/dnmtools:uniq-max-buffer-sizeCopy head branch name to clipboardDec 12, 2023

+393-61

Commits

Commits on Dec 9, 2023

• xcounts: adding code to get a header from a fasta reference genome file

  andrewdavidsmith

  committed
  b786395

• xcounts: testing some threading issues

  andrewdavidsmith

  committed
  09eea21

• several source files: checking that input file is BGZF format before using the threadpool for decompression

  andrewdavidsmith

  committed
  048408e

• bamxx submodule update

  andrewdavidsmith

  committed
  f658558

• xcounts: fixing a bug from previous commit

  andrewdavidsmith

  committed
  5b3568a

• unxcounts: including logic to verify header against chromosomes sequences currently just using length

  andrewdavidsmith

  committed
  f50caba

• unxcounts: adding logic to only generate the counts for covered sites

  andrewdavidsmith

  committed
  16a3fdc

• xcounts: ignoring the mutation mark on sites

  andrewdavidsmith

  committed
  2583dc8

• unxcounts: better error message on inconsistent header

  andrewdavidsmith

  committed
  84846ce

• unxcounts: trying to find the best header termination

  andrewdavidsmith

  committed
  3edadb1

• unxcounts: better handling of header

  andrewdavidsmith

  committed
  fd39ce8

• xcounts and counts: header no longer ends with end_header and also there is no space after the # in header lines

  andrewdavidsmith

  committed
  6db3e53

• unxcounts: fixing backwards condition for requiring coverage

  andrewdavidsmith

  committed
  76ecc8c

• unxcounts: adding a missed spot to check for required coverage

  andrewdavidsmith

  committed
  944e660

• counts_header.cpp counts_header.hpp Makefile.am: adding counts_header stuff

  andrewdavidsmith

  committed
  0e329e9

• MSite.cpp: adding a loop to pass the header when trying to determine if a file is a counts file

  andrewdavidsmith

  committed
  2bfcef0

• hmr.cpp and pmd.cpp: adding code to skip the header when reading sites

  andrewdavidsmith

  committed
  dd6cb9d

• methcounts.cpp: refactoring to move the header code into counts_header.chpp

  andrewdavidsmith

  committed
  699a0f2

• recovered.cpp: refactoring to move the header stuff into counts_header

  andrewdavidsmith

  committed
  edeb17d

• smmetric-cpgs.cpp: refactoring to move the header stuff into counts_header

  andrewdavidsmith

  committed
  c13c28d

• xcounts.cpp: refactoring to move the header stuff into counts_header

  andrewdavidsmith

  committed
  1e1707c

• unxcounts.cpp: refactoring to move the header stuff into counts_header

  andrewdavidsmith

  committed
  6acba7b

Commits on Dec 12, 2023

• uniq.cpp: adding a variable to control the max buffer size which matters for some strange data sets with hundreds of thousands of reads at the same mapping location

  andrewdavidsmith

  committed
  32fd022