Skip to content

Latest commit

 

History

History
143 lines (112 loc) · 3.38 KB

CHANGES.md

File metadata and controls

143 lines (112 loc) · 3.38 KB

v0.3.26 (dev)

  • fix for hts_idx_set_meta (#86)

v0.3.25

  • new smaller docker image (#85)

v0.3.19

  • [vcf] allow using vcf.set_samples(@["^"]) to remove all samples

v0.3.18

  • [vcf] fix for #77 for to avoid double-free of header when it's re-used.

v0.3.17

  • turn quits into exceptions

v0.3.16

  • expose VCF.fname
  • change rendering of unknown alleles to fix './.'

v0.3.15

  • vcf: expose a couple more functions from htslib

v0.3.14

  • add close method to fai for consistency (continues to also occur automatically upon garbage collection) #70

v0.3.13

  • changes for nim ORC/ARC GCs

v0.3.11

  • add bgzi.open which allows opening for reading and writing without quit() and replaces wopen_bgzi and ropen_bgzi

v0.3.9

  • add newCigar(els: seq[CigarElement]): Cigar (#9)

v0.3.8

  • flush stdout on destroy_vcf

v0.3.7

  • fix bai creation in xam_index

v0.3.6

  • automatically set cram or bam file-type for file opened in write mode based on file extension (#64)

v0.3.5

  • add xam_index to index bam and cram files.

v0.3.4

  • hts/vcf Variant.alts will report sum of known alt alleles for ploidy greater than 2.

v0.3.3

  • report contig length if available in vcf.contigs (#51)

v0.3.2

  • allow specifying "*" or "-3" for the chromosome in vcf.query to iterator over entire file.

v0.3.1

v0.3.0

  • breaking change update to htslib 1.10. this is a breaking change and will require htslib 1.10 or higher. if hts-nim detects a version of < 1.10, it will generate an error
  • add htslibVersion() function which returns a string of the version reported by htslib
  • bam/Target is no longer a ref object (this will affect almost noone)

v0.2.23

  • hts/bam fix from_string for bam record and header. See quinlan-lab/STRling#10
  • hts/files add fname.file_type to get the file type given a path

v0.2.22

  • changes for latest nim
  • fix several memory leaks in rarely-used functions

v0.2.21

  • hts/vcf allow setting id.
  • hts/vcf flush stdout on close.
  • hts/bam correct check for EOF (#48)
  • hts/bam better error message for error in interation

v0.2.20

  • hts/files (iterate over bgzipped or text files identically)

v0.2.16

  • [bam] add set_qname

v0.2.14

  • [vcf] add format.delete to delete format (sample) fields from vcf records. v0.2.12 =======
  • [bam] optimize cigar. had extra calls and memory-use.

v0.2.11

  • [vcf] more lazy about unpack; gives some performance improvement
  • [vcf] use pointer size to allow better memory re-use.

0.2.9

  • [vcf] unpack after copy. this was causing hard-to-diagnose problems whenever Variant.copy was used.

0.2.8

  • [vcf] allow writing from a VCF that does not contain contigs (in htslib this is an error)
  • [vcf] fix bug in getting (absent) string arguments from INFO.

v0.2.7

  • [vcf] remove deprecated FORMAT (ints, floats) and INFO (ints, floats, strings)
  • [vcf] add FORMAT.get, set(field, strings) to get and set string fields from FORMAT fields
  • [vcf] add FORMAT.fields to iterate for the FORMAT field of a VCF, the returned FormatField type tells the name, (v)type and number of values per sample of each field.

v0.2.5

  • [vcf] deprecate ints, strings, floats in favor of dispatch to get for both INFO and FORMAT.