0.7.0

See change log

0.6.0

BREAKING

• N padding for out-of-range bases is not appended. See #120 (comment) and #121 for more information.
• cljam.io.protocols/{reader,writer}-path were renamed to cljam.io.protocols/{reader,writer}-url. Their return values are java.net.URL.

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
• Add some BED manipulation APIs. #131
• Support more source types. #132

Changed

• Remove N padding for out-of-range bases in read-sequence. #121
• Upgrade dependencies. #134

Fixed

• Fix some serialization functions. #122
• Fix parsing SAM header values containing ':'. #123
• Fix wrong padding of last bases in 2bit writer. #127
• Fix a bug in merging bed regions. #130
• Fix exec binary on Java 9+. #133

0.5.1

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

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

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

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

• Remove dependency on raynes/fs. #80
• Improve sorter. #81
• Namespace refactoring. #83
• I/O API refactoring. #84
• Use proton instead of some utilities. #87

Fixed

• Fix test of BCF writer. #82

0.3.1

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

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

0.2.1

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

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