Pairix Versions Save

Fix for standard C library's discontinued support of implicit function declarations.

• 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.

• 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).

• Backward compatible with an old index (generated by version 0.2.5-0.3.3)

• The maximum chromosome size allowed is now 2^30 instead of 2^29 with new index. Index structure changed.

• The problem of pypairix get_blocknames crashing python when called twice now fixed.

• 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.

• 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).

• 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.

• 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.