Commits · 28c58f7916a36b6b7fc517392db7be4d1f3dd938 · github_fork / Chromap · GitLab

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Apr 21, 2022
- Use a char for range strand. · 28c58f79
  Haowen Zhang authored Apr 20, 2022
  
  28c58f79
- Remove a useless class variable for ranges. · 3639e685
  Haowen Zhang authored Apr 20, 2022
  
  3639e685
- Format code. · 5710d90e
  Haowen Zhang authored Apr 20, 2022
  
  5710d90e
- Use multiple read format fields to specify non-consecutive sequence. Fix several bugs in parsing. · 34905b18
  Li authored Apr 20, 2022
  
  34905b18
- Add more space and brackets. · de5470ae
  Haowen Zhang authored Apr 19, 2022
  
  de5470ae
- Rename sequence effective range variables. · de54d9b2
  Haowen Zhang authored Apr 19, 2022
  
  de54d9b2
- Make char int conversion functions free. · c7ba742a
  Haowen Zhang authored Apr 19, 2022
  c7ba742a
- Update README · 2169e0f5
  Li authored Apr 18, 2022
  
  2169e0f5
- Allow the specification of non-consecutive sequence range usage through --read-format · 7556c47b
  Li authored Apr 18, 2022
  
  7556c47b
Apr 15, 2022
- Update version. · 148082f7
  Haowen Zhang authored Apr 15, 2022
  
  View commits for tag v0.2.2 v0.2.2
  
  148082f7
- Fix a bug and format code. · 854db086
  Haowen Zhang authored Apr 14, 2022
  
  854db086
- Fix an issue of missing adapter trimming due to tandem repeat near read start. · a094dd49
  Li authored Apr 11, 2022
  
  a094dd49
- Fix a typo when doing the final trimming · 4b2aba6c
  Li authored Apr 11, 2022
  
  4b2aba6c
- Allow containment in adapter trimming · d9758ea8
  Li authored Apr 03, 2022
  
  d9758ea8
Mar 29, 2022
- Improve code readability. · bfb95030
  Li authored Mar 27, 2022
  
  bfb95030
- Properly handle the Ns in the barcode during barcode correction. · 09e23ef1
  Li authored Mar 27, 2022
  
  09e23ef1
- Replace N by T if reverse complemented to make sure the results is consistent... · d5359b7d
  Li authored Mar 25, 2022
  d5359b7d
- Do not do the reverse-complement operation on the quality score when reversing. · 59e405c3
  Li authored Mar 25, 2022
  
  59e405c3
Mar 25, 2022
- Introduce an in memory mapping layout. · 9b64a21c
  Haowen Zhang authored Mar 24, 2022
  9b64a21c
- Add missing headers. · 0193ab5a
  Haowen Zhang authored Mar 24, 2022
  
  0193ab5a
- Add an todo for sam. · 1cca730f
  Haowen Zhang authored Mar 24, 2022
  
  1cca730f
- Code refactor. · 56978391
  Haowen Zhang authored Mar 23, 2022
  56978391
- Remove some unused code. · 92ecd0ad
  Haowen Zhang authored Mar 23, 2022
  
  92ecd0ad
- Clean code and add const or space when needed. · 4741ebd3
  Haowen Zhang authored Mar 23, 2022
  
  4741ebd3
- Format code. · c6d9e3ba
  Haowen Zhang authored Mar 23, 2022
  
  c6d9e3ba
- Remove manual mem allocation for heap sort. · a8f9f599
  Haowen Zhang authored Mar 22, 2022
  
  a8f9f599
- Format code for index. · 70059f8f
  Haowen Zhang authored Mar 22, 2022
  
  70059f8f
- Short parameter list for index construction. · 3812b8e6
  Haowen Zhang authored Mar 22, 2022
  3812b8e6
Mar 22, 2022
- Update version for a new release. · 36a05469
  Haowen Zhang authored Mar 21, 2022
  
  View commits for tag v0.2.1 v0.2.1
  
  36a05469
- Avoid passing too many parameters for verification. · 67d67814
  Haowen Zhang authored Feb 26, 2022
  
  67d67814
- Add some comment for force mapq. · 5afc489a
  Haowen Zhang authored Feb 25, 2022
  
  5afc489a
- Avoid passing too many parameters. · 0ec61ada
  Haowen Zhang authored Feb 25, 2022
  0ec61ada
Mar 20, 2022
- Fix gcc conversion warning. · d6e244e1
  Haowen Zhang authored Mar 09, 2022
  
  d6e244e1
- Fix warnings with clang and a wrong type conversion. · 3ff43093
  Haowen Zhang authored Mar 09, 2022
  
  3ff43093
- Change resize0 to clear. · 38164cf2
  Li authored Mar 18, 2022
  
  38164cf2
- Still use 64bit candidate sort. Further do not cache near the beginning. · 7d6be693
  Li authored Mar 18, 2022
  
  7d6be693
- Fix a problem of underflow causing wrong hit order · 8806e956
  Li authored Mar 13, 2022
  
  8806e956
- Adjust cache update threshold. · 450e04df
  Li authored Mar 09, 2022
  
  450e04df
- Do not cache the alignments near the beginning of a chromosome. Adjust the... · d0334577
  Li authored Mar 09, 2022
  d0334577
- Handle the case in cache that may underflow when shifting at beginning of ref 0. · 0ccd2c7a
  Li authored Mar 04, 2022
  
  0ccd2c7a

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