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feat: added per-read flag and map quality filtering #194

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feat: added per-read flag and map quality filtering #194

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Commits on Sep 19, 2024

  1. fix: CMake build errors on Mac resolved 

     - closes griffithlab#176, CMake was including `src/utils/bedtools/gzstream/version`
   as a C++ source file, when it was a simple text file containing version info
 - I moved this version info into `src/utils/bedtools/gzstream/README`
    @TimD1
    TimD1 committed Sep 19, 2024
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  2. fix: min_intron_length_ initialization in JunctionsExtractor 

     - fixes griffithlab#188, min_intron_length_ was accidentally set from min_anchor_len_
    @TimD1
    TimD1 committed Sep 19, 2024
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  3. feat: added per-read flag and map quality filtering 

     - closes griffithlab#183, flag based filtering
 - closes griffithlab#189, mapping quality based filtering
 - option '-F' filters reads containing any of these flags
 - option '-f' filters reads not containing all these flags
 - option '-q' filters reads below this mapping quality
    @TimD1
    TimD1 committed Sep 19, 2024
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