Changelogs » Methylpy

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Methylpy

1.2.9

Fix a bug in merging allc files when there are too many input allc files

1.2.5

Release tutorial
  Fix a bug in allc-to-bigwig

1.2.4

Fix a bug in generating SNP info

1.2.3

Fix bug in help information due to percent symbol

1.2.2

Update DMRfind to make sure to filter out DMRs with all sample categories assigned to the same side (all hypo- or all hyper-)

1.2.1

Fix bug on DMRfind due to modification on filter-allc

1.2.0

* Add options to apply SNP filter on allc files using filter-allc
  * Add multiprocess option in filter-allc
  * Add merge snp information option in merge-allc
  * Change the default of --min-mapq to 30
  * Minor bug fixed

1.1.9

Fix bug regarding to --add-snp-info

1.1.8

* fix bug regarding --add-snp-info
  * add --min-mapq option to filter out reads with low mapping quality

1.1.7

Fix bin_size issue in --allc-to-bigwig

1.1.6

Fix issue in counting unconverted and converted basecalls when indel is present
  
  add option `--add-snp-info` to include two additional columns in allc files to reflect genotype information

1.1.5

Fix bugs when methylpy processes reads over 250bp long

1.1.4

Fix bugs and add code for error handling

1.1.1

* Fix chr prefix issue in allc-to-bigwig
  * Change the default to False for --remove-clonal in processing pipeline
  * Change cytosine position encoding to allow the processing long reads

1.1.0

Allows speeding up merge-allc using multiple processors
  methylpy now uses multithread feature of samtools
  Optimized the manipulation of allc index
  Fixed bugs

1.0.11


        

1.0.10

methylpy indexes allc files for faster accessing.
  
  merge-allc function is optimized and runs faster.