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Releases: 4dn-dcic/pairix

0.3.8

02 Feb 13:55
94d0107
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Fix for standard C library's discontinued support of implicit function declarations.

0.3.7

11 Apr 14:56
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  • The issue with integer overflow with get_linecount of pypairix is now fixed. (no need to re-index).
  • Fixed issue where autoflip causes segmentation fault or returns an empty result on some systems. This affects pairix -Y, pairix -a, pypairix.check_triangle() and pypairix.querys2D(). It does not affect the results on 4DN Data Portal.

0.3.6

30 Apr 17:30
07bcab0
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  • Line count (pairix -n) integer overflow issue has been fixed. The index structure has changed. The index generated by the previous versions (0.2.5 ~ 0.3.3, 0.3.4 ~ 0.3.5) can be auto-detected and used as well (backward compatible).

0.3.5

21 Mar 18:08
9e0d8cc
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  • Backward compatible with an old index (generated by version 0.2.5-0.3.3)

0.3.4

15 Mar 17:26
a181178
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  • The maximum chromosome size allowed is now 2^30 instead of 2^29 with new index. Index structure changed.

0.3.3

16 Nov 22:32
d74b4f8
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  • The problem of pypairix get_blocknames crashing python when called twice now fixed.

0.3.2

27 Oct 19:48
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  • pairix -Y option is now available to check whether a pairix-indexed file is a triangle (i.e. a chromosome pair occurs in one direction. e.g. if chr1|chr2 exists, chr2|chr1 doesn't)
  • pypairix check_triangle function is also now available to check whether a pairix-indexed file is a triangle.
  • pairix -B option is now listed as part of the usage.

0.3.1

24 Oct 18:22
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  • pairix -B option is now available to print out the number of bgzf blocks for each chromosome (pair).
  • The same function is available for pypairix (bgzf_block_count).

0.3.0

04 Oct 16:20
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  • The problem with fragment_4dnpairs.pl of adding an extra column is now fixed.
  • 1D querying on 2D data now works with pypairix
  • Some test fixes.

0.2.9

02 Oct 18:58
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  • pairix can now take 1D query for 2D data. e.g.) pairix file.gz 'chr22:50000-60000' is equivalent to pairix file.gz 'chr22:50000-60000|chr22:50000-60000' if file.gz is 2D indexed.