Code

Bcftools ploidy#133

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martinghunt merged 32 commits intosanger-pathogens:mastersanger-pathogens/ariba:masterfrom martinghunt:bcftools_ploidymartinghunt/ariba:bcftools_ploidyCopy head branch name to clipboardAug 31, 2016

+11,985-461

Commits

Commits on Aug 24, 2016

• replace bcftools with own c++ version that keeps minor alleles

  

  Martin Hunt

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  70d8335

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• Remove unneeded tbi file

  

  Martin Hunt

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  d3168fb

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Commits on Aug 25, 2016

• Depths file has total per contig, no need to total them up

  

  Martin Hunt

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  79debe1

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• Store name of contigs depth file

  

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  cd37674

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• rm contig depths file

  

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  61505ab

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• Update to use new samtools_variants options

  

  Martin Hunt

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  60ee502

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• Remove bcftools

  

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  d5ba3a1

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• Use pysam.faidx instead of syscall to samtools

  

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  6a8a274

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• Remove unused options

  

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  002ea3c

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• Use pysam for mapping instead of syscalls to samtools

  

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  910051f

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• Remove best_seq_chooser, done with mash instead

  

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  ccdaadc

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• Use pysam instead of syscall to mpileup

  

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  c770974

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• Remove samtools dependency (use pysam)

  

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  33eff8c

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• Remove unused imports

  

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  129579e

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• Remove unused import sys

  

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  819b930

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• Remove unused imports

  

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  69443ee

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• Mention required python packages

  

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  0637720

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• require pysam >= 0.9.1

  

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  e770715

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• Min python 3.3.2

  

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  b62be43

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• More persmissive with input format

  

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  055b8c4

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• Remove unused options

  

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  2f4a015

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• faidx first, to stop fa_load messages to stderr

  

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  f9bd4d9

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• Drop max_allele_freq to 90

  

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  cbaf51d

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• Add min sceond allele depth = 2

  

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  c5f378c

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• Bug fix checking second allele depth

  

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  14674da

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Commits on Aug 26, 2016

• new method _depths_look_het

  martinghunt

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  6511dd7

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• remove debug prints

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  a7c00b5

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• New class attribute is_het

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  908db38

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• Get alt base from ref_ctg_change first if possible

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  6baa93f

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• Add test of whole run of summary

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  ddc7adc

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Commits on Aug 30, 2016

• Add note about bowtie2-build

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  38efcf8

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• Remove genetic code option from getref

  martinghunt

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  18ed4c8

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