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Changelog

0.3.0

  • Updated the phenotyper() method for the CYP2C9 gene (#18).
  • Changed the function of CYP2C9*3 in star_table.tsv from decreased function to no function.
  • Updated the calculate-read-depth command to accept single BAM file as input (#19).

0.2.0

  • From now on, pypgx will be hosted on Anaconda instead of PyPI. This is because pypgx needs access to many non-Python programs and these are not available via PyPI.
  • Updated the license from GPL-3.0 License to MIT License.
  • Temporarily removed all the of commands except bam2vcf2, bam2gdf, and compgt. Some of the removed commands will be brought back in the later versions.
  • The bam2vcf2 command has been renamed as call-variants-gatk-sge.
  • The bam2gdf command has been renamed as calculate-read-depth.
  • The compgt command has been renamed as compare-stargazer-calls.

0.1.37

  • Removed dependency to the vcfgo package.
  • Removed the mergevcf command.

0.1.36

  • Updated NUDT15 phenotype (#9).

0.1.35

  • Updated phenotypes for TPMT, UGT1A1, and DPYD (#5).

0.1.34

  • Added a new configuration parameter called conda_env.
  • Added a conda recipe (conda/stargazer-conda.yml) for Stargazer environment.

0.1.33

  • No significant changes.

0.1.32

  • No significant changes.

0.1.31

  • No significant changes.

0.1.30

  • cpa command has been deprecated.

0.1.29

  • Added unicov tool.

0.1.28

  • plotcov command has been deprecated.

0.1.27

  • Bumped up the minimally required version of vcfgo (0.0.3 to 0.0.4).
  • Added unit tests.

0.1.26

  • Integrated Python module vcfgo to peek command.
  • Integrated Python module vcfgo to viewsnp command.

0.1.25

  • Integrated Python module vcfgo to minivcf command.
  • Integrated Python module vcfgo to merge command.
  • Renamed merge.py to mergevcf.py.

0.1.24

  • Integrated Python module vcfgo to compvcf command.

0.1.23

  • [#4] Fixed bug when using bam2gdf for the GSTT1 gene with hg38 data.

0.1.22

  • No significant changes.

0.1.21

  • No significant changes.

0.1.20

  • No significant changes.

0.1.19

  • No significant changes.

0.1.18

  • No significant changes.

0.1.17

  • No significant changes.

0.1.16

  • Updated compvcf.py to also output sample names.

0.1.15

  • Added compvcf tool.

0.1.14

  • No significant changes.

0.1.13

  • No significant changes.

0.1.12

Updated compare2 to also output the target gene column.

0.1.11

  • Updated bam2gt2 to accept a list of reference samples.

0.1.10

  • Added compare2 tool.

0.1.9

  • Added -q 1 argument to bcftools caller in bam2vcf.py.

0.1.8

  • No significant changes.

0.1.7

  • No significant changes.

0.1.6

  • Updated sgep.py to support multiple target genes. Consequently, xgep.py was removed.
  • Renamed sgep.py to bam2gt2.py.

0.1.5

  • Updated sgep.py to support both GATK (bam2vcf2.py) and BCFtools (bam2vcf.py).

0.1.4

  • Added bam2vcf2.py (a SGE-based version of bam2vcf.py specifically for gatk caller).

0.1.3

  • Added GATK argument java_options to bam2vcf.py.

0.1.2

  • No significant changes.

0.1.1

  • Renamed report.py to gt2html.py.
  • Renamed remap.py to bam2bam.py.
  • Renamed sges.py to bam2html.py

0.1.0

  • Renamed genotype.py to bam2gt.py.
  • The new bam2vcf.py can support both GATK and BCFtools for SNP calling.
  • The new sgep.py and xgep.py can support both GATK and BCFtools for SNP calling. Consequently, sgea.py and xgea.py were removed.

0.0.80

  • Added bam2vcf2.py (which will replace bam2vcf.py in near future).

0.0.79

  • Updated sgep.py, xgep.py and sges.py.

0.0.78

  • Replaced HaplotypeCaller with BCFtools for sges.py and sgep.py.

0.0.77

  • Added xgea tool.

0.0.76

  • Added xgep tool.

0.0.75

Fixed a bug in the Drugs section for report.py.

0.0.74

  • Fixed incorrect argument setting for BAM files.

0.0.73

  • Updated report.py and gt2pt.py.

0.0.72

  • Updated summary.py and meta.py.

0.0.71

  • Updated gt2pt.py for CYP2C19 gene.

0.0.70

  • Added gt2pt tool (only supports CYP2D6 gene for now).

0.0.69

  • Updated bam2gdf.py and bam2vcf.py.

0.0.68

  • Updated sgea.py.

0.0.67

  • Updated sgep.py.

0.0.66

  • Updated sges.py and report.py.

0.0.65

  • Updated genotype.py.

0.0.64

  • Updated genotype.py.

0.0.63

  • Added genotype tool.

0.0.62

  • Updated bam2vcf.py.

0.0.61

  • Updated bam2vcf.py.

0.0.60

  • Added elapsed run time to logging.

0.0.59

  • Added bam2vcf tool.

0.0.58

  • No significant changes.

0.0.57

  • Updated report.py.

0.0.56

  • Updated fq2bam.py and remap.py.

0.0.55

  • No significant changes.

0.0.54

  • Increased compatibility with Stargazer.

0.0.53

  • Updated sglib.py.

0.0.52

  • No significant changes.

0.0.51

  • No significant changes.

0.0.50

  • No significant changes.

0.0.49

  • No significant changes.

0.0.48

  • Updated bam2gdf tool to support hg38.

0.0.47

  • Updated configuration parameters.

0.0.46

  • Added VCF only mode to sges tool.

0.0.45

  • Added VCF only mode to sgea tool.

0.0.44

  • Added VCF only mode to sgep tool.

0.0.43

  • No significant changes.

0.0.42

  • Added sglib.py.

0.0.41

  • No significant changes.

0.0.40

  • No significant changes.

0.0.39

  • Added snp tool.

0.0.38

  • Added peek tool.

0.0.37

  • Added liftover tool.

0.0.36

  • Added check tool.

0.0.35

  • Added plotcov tool.

0.0.34

  • No significant changes.

0.0.33

  • Added cpa tool.

0.0.32

  • Added sges tool.

0.0.31

  • Added sgep tool.

0.0.30

  • Added sgea tool.

0.0.29

  • Added fq2bam tool.

0.0.28

  • Added remap tool.

0.0.27

  • Added compare tool.

0.0.26

  • No significant changes.

0.0.25

  • Added meta tool.

0.0.24

  • Added summary tool.

0.0.23

  • No significant changes.

0.0.22

  • No significant changes.

0.0.21

  • No significant changes.

0.0.20

  • Added version.py.

0.0.19

  • Updated VCFFile class.

0.0.18

  • Added merge tool.

0.0.17

  • Added minivcf tool.

0.0.16

  • No significant changes.

0.0.15

  • Added Read the Docs.

0.0.14

  • Added type hints.

0.0.13

  • Added bam2gdf tool.

0.0.12

  • Added bam2sdf tool.

0.0.11

  • Added sdf2gdf tool.

0.0.10

  • Updated pgkb tool to be run within Python.

0.0.9

  • No significant changes.

0.0.8

  • No significant changes.

0.0.7

  • Added report tool.
  • Added resources directory.

0.0.6

  • No significant changes.

0.0.5

  • No significant changes.

0.0.4

  • Added pgkb tool.

0.0.3

  • Added common.py.

0.0.2

  • No significant changes.

0.0.1

  • Initial release.