0.3.0

BREAKING

From this release, cljam.vcf/read-variants parses FORMAT, FILTER, INFO and samples columns of VCF.

(require '[cljam.vcf :as vcf])

(with-open [rdr (vcf/reader "test-resources/vcf/test-v4_3.vcf")]
  (first (vcf/read-variants rdr)))
;;=> {:FORMAT (:GT :GQ :DP :HQ),
;;    :NA00001 {:DP 1, :GQ 48, :GT "0|0", :HQ (51 51)},
;;    :NA00002 {:DP 8, :GQ 48, :GT "1|0", :HQ (51 51)},
;;    :NA00003 {:DP 5, :GQ 43, :GT "1/1", :HQ (nil nil)},
;;    :alt ["A"],
;;    :chr "20",
;;    :filter (:PASS),
;;    :id "rs6054257",
;;    :info {:AF (0.5), :DB :exists, :DP 14, :H2 :exists, :NS 3},
;;    :pos 14370,
;;    :qual 29.0,
;;    :ref "G"}

Add {:depth :vcf} option to the second argument if string is preferred.

Added

• Add a function to clone bam reader. #39
• Support coverage analysis with cloverage. #45
  • Integration with Codecov. #46
  • Reduce worktime of coverage. #69
• Add many tests. #60
• Add tests to check generated data correctness. #61
  • Examine result file of dedupe in test. #63
  • Examine result file of create-dict in test. #64
  • Examine result files of cljam pileup in test. #65
  • Examine result file of cljam normalize in test. #66
  • Examine result file of create-mpileup. #67
  • Examine result file of cljam level test. #70
• Add BCF reader/writer and utility functions for VCF. #68

Changed

• Improves performance of pileup. #41
• Migrate from midje to clojure.test. #44
• Correct base qualities if reads are overlapped. #47
• Use lein-binplus instead of lein-bin. #48
• Add marks to private fn. #50
• Refine unused code for newline. #51
• Pileup without options. #54
• Refine trim-chromosome-key. #55
• Refine fastq-char->phred-byte / Add phred-byte->fastq-char. #56
• Separate test resources based on file types. #71
• Separate :slow and :heavy test-selectors. #72

Fixed

• Fix for create-mpileup. #52
• Fix for cljam level command. #57