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CHANGELOG.md

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Change Log

Unreleased

Added

  • Add some extensions for FASTA format. #124
  • Add many util functions for SAM/BAM files & split cljam.io.sam.util. #128
  • Add FASTQ=>FASTA, SAM=>FASTQ conversions. #129

Changed

  • Remove N padding for out-of-range bases in read-sequence. #121

Fixed

  • Fix some serialization functions. #122
  • Fix parsing SAM header values containing ':'. #123
  • Fix wrong padding of last bases in 2bit writer. #127

0.5.1 - 2017-11-10

Added

  • Set up benchmarks. #108
  • Add read-indices to ISequenceReader protocol. #109
  • Extract region utils to cljam.util.region and add some functions. #110
  • Add region option to view command. #112
  • Add FASTA-TwoBit converter. #117

Changed

  • Make convert parallelism controllable. #113
  • Java 9 compatibility. #114
  • Move coverage phase to build stages. #116
  • Low-memory sequence I/O. #118
  • Improve performance of FASTA random reading. #120

Fixed

  • Fix StackOverflowError in cljam.io.protocols/read-in-region. #107
  • Fix parsing comma-separated number in region. #111
  • Don't refer clojure.core/indexed? in cljam.io. #115
  • Fix a bug that 2bit reader incorrectly reads small n. #119

0.5.0 - 2017-09-05

BREAKING

  • :ignore-index option of cljam.io.sam/bam-reader and cljam.io.sequence/fasta-reader is removed.
  • :depth option of cljam.io.sam/read-alignments is removed. It returns SAMAlignment only.
  • SAM/BAM reading functions return Eduction instances instead of lazy sequences.

Added

  • Add a logging configuration for cli. #99
  • Add an ordering function for chromosome name. #101
  • Add utilities for whole-genome coordinate. #103

Changed

  • Refactor cljam.algo.level. #93
  • Refactor BAI I/O. #96
  • Reorganize BAM I/O. #97
  • Tweak the normalization function for chromosome name. #98
  • Make index reading of FASTA reader delayed. #100
  • Improve sequence readers. #104
  • Rename test namespaces to conventional names. #105
  • Upgrade dependencies. #106

Fixed

  • Update an example usage of depth in README. #94
  • Use returned values of conj! in reg->bins*. #95
  • Use lazy pmap for lazy-depth. #102

0.4.1 - 2017-08-01

Changed

  • Improve chromosome normalization. #89
  • Suppress log output in test. #90
  • Extract depth algorithm and improve performance. #91

Fixed

  • Fix parser of optional fields in SAM/BAM. #92

0.4.0 - 2017-06-28

BREAKING

Namespaces of most APIs are changed in this release.

  • cljam.io.*** - reader/writer functions of various formats such as SAM, VCF, and FASTA.
  • cljam.algo.*** - algorithms such as sort, indexing, and pileup.
  • cljam.util.*** - utilities such as chromosome name normalization.
  • cljam.tools.*** - tools such as command-line interface.

Added

  • Add protocols for I/O APIs. #78
  • Add FASTAWriter and TwoBitWriter. #79
  • Support SAM normalization. #86
  • Add docstring. #88

Changed

Fixed

  • Fix test of BCF writer. #82

0.3.1 - 2017-05-29

Added

  • Add BED reader/writer. #73

Changed

  • Change default start/end of bam reader. #74
  • Extend cljam.core reader/writer functions. #75
  • Setup automatic snapshots deployment. #76
  • Improve performance of deep decoding of BAM files. #77

0.3.0 - 2017-05-08

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
  • 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

0.2.1 - 2017-04-06

Added

  • 2bit-encoded reference reader. #31
  • Add functions for deduplicating paired-end BAM. #32
  • Add :ignore-index option to cljam.fasta/reader. #34

Changed

  • Improve performance of FASTA indexing. #30
  • Improve performance of BAM sequence encoding. #35

Fixed

  • Fix cider-refresh error. #33
  • Fix StackOverflowError in parse-header of SAM/BAM files. #38

0.2.0 - 2017-02-20

BREAKING

From this release, ranges are represented as one-based closed intervals. For example,

{:chr "chr1", :start 1, :end 3}

represents the first three bases of chromosome 1.

Added

  • BED file reader/writer. #20
  • Read unplaced reads in BAM. #24

Changed

  • Improve performance of reading BAM files. #22
  • Replace candidate-message function with one in clj-sub-command.
  • Improve performance of reading vcf file. #29

Fixed

  • Fix a bug in BAM random reader. #21
  • Read multiple contigs in VCF meta info. #23 #25
  • Enable decompressUntilEOF of CompressorStreamFactory. #26
  • Fix bugs in mpileup. #27 #28

0.1.6 - 2017-01-06

  • Sequential reading function for FASTA #16
  • Common compressor stream #17
  • Add encode/decode functions for SAM FLAG field #19
  • Fix mpileup bug
  • Improve project settings #18

0.1.5 - 2016-07-26

  • Add FASTQ I/O
  • Add VCF I/O
  • Improve level analyzer
  • Improve mpileup
  • Improve performance of SAM/BAM conversion
  • Fix bugs of sorter
  • Fix small bugs

0.1.4 - 2016-02-02

  • Add level analyzer of alignments
  • Update dependencies except clojure 1.8.0
  • Enable CI with JDK8
  • Fix bugs of sorter
  • Fix bugs of m-pileup
  • Fix small bugs

0.1.3 - 2015-08-14

  • Improve FASTA reading
  • Improve normalization
  • Improve pileup performance (also support concurrency)
  • Enable index command to specify the number of threads
  • Display sub-command candidates
  • Fix bugs

0.1.2 - 2014-05-20

  • Improve performance of pileup
  • Fix small bugs
  • Refactoring codes

0.1.1 - 2014-04-25

  • Improve performance of BAM indexing
  • Fix bugs of FASTA indexing
  • Fix bugs of sequence dictionary creation
  • Refactoring codes

0.1.0 - 2014-04-03

First release