{"action":"opened","issue":{"url":"https://api.github.com/repos/pysam-developers/pysam/issues/106","labels_url":"https://api.github.com/repos/pysam-developers/pysam/issues/106/labels{/name}","comments_url":"https://api.github.com/repos/pysam-developers/pysam/issues/106/comments","events_url":"https://api.github.com/repos/pysam-developers/pysam/issues/106/events","html_url":"https://github.com/pysam-developers/pysam/issues/106","id":68118726,"number":106,"title":"get_aligned_pairs semantics changed. was this intentional?","user":{"login":"timodonnell","id":467896,"avatar_url":"https://avatars.githubusercontent.com/u/467896?v=3","gravatar_id":"","url":"https://api.github.com/users/timodonnell","html_url":"https://github.com/timodonnell","followers_url":"https://api.github.com/users/timodonnell/followers","following_url":"https://api.github.com/users/timodonnell/following{/other_user}","gists_url":"https://api.github.com/users/timodonnell/gists{/gist_id}","starred_url":"https://api.github.com/users/timodonnell/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/timodonnell/subscriptions","organizations_url":"https://api.github.com/users/timodonnell/orgs","repos_url":"https://api.github.com/users/timodonnell/repos","events_url":"https://api.github.com/users/timodonnell/events{/privacy}","received_events_url":"https://api.github.com/users/timodonnell/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-04-13T14:56:28Z","updated_at":"2015-04-13T14:56:28Z","closed_at":null,"body":"The 1e2d96d578a94762da7d647cacec98e81c10263a revision appears to have introduced a change in semantics for `get_aligned_pairs`. Before that revision, the read offsets were with respect to the non-soft-clipped part of the sequence (i.e. offsets into `query_alignment_sequence`). After that change they seem to be offsets into the full sequence (i.e. `query_sequence`). Was this change intentional?\r\n\r\nFor example, for an alignment with cigar string `5S96M`, the old behavior was to give:\r\n\r\n```\r\n[[(0, 10006730), (1, 10006731), (2, 10006732), (3, 10006733), (4, 10006734), (5, 10006735), (6, 10006736), (7, 10006737), (8, 10006738), (9, 10006739), (10, 10006740), (11, 10006741), (12, 10006742), (13, 10006743), (14, 10006744), (15, 10006745), (16, 10006746), (17, 10006747), (18, 10006748), (19, 10006749), (20, 10006750), (21, 10006751), (22, 10006752), (23, 10006753), (24, 10006754), (25, 10006755), (26, 10006756), (27, 10006757), (28, 10006758), (29, 10006759), (30, 10006760), (31, 10006761), (32, 10006762), (33, 10006763), (34, 10006764), (35, 10006765), (36, 10006766), (37, 10006767), (38, 10006768), (39, 10006769), (40, 10006770), (41, 10006771), (42, 10006772), (43, 10006773), (44, 10006774), (45, 10006775), (46, 10006776), (47, 10006777), (48, 10006778), (49, 10006779), (50, 10006780), (51, 10006781), (52, 10006782), (53, 10006783), (54, 10006784), (55, 10006785), (56, 10006786), (57, 10006787), (58, 10006788), (59, 10006789), (60, 10006790), (61, 10006791), (62, 10006792), (63, 10006793), (64, 10006794), (65, 10006795), (66, 10006796), (67, 10006797), (68, 10006798), (69, 10006799), (70, 10006800), (71, 10006801), (72, 10006802), (73, 10006803), (74, 10006804), (75, 10006805), (76, 10006806), (77, 10006807), (78, 10006808), (79, 10006809), (80, 10006810), (81, 10006811), (82, 10006812), (83, 10006813), (84, 10006814), (85, 10006815), (86, 10006816), (87, 10006817), (88, 10006818), (89, 10006819), (90, 10006820), (91, 10006821), (92, 10006822), (93, 10006823), (94, 10006824), (95, 10006825)]]\r\n```\r\n\r\nand the new behavior:\r\n\r\n```\r\n[[(0, None), (1, None), (2, None), (3, None), (4, None), (5, 10006730), (6, 10006731), (7, 10006732), (8, 10006733), (9, 10006734), (10, 10006735), (11, 10006736), (12, 10006737), (13, 10006738), (14, 10006739), (15, 10006740), (16, 10006741), (17, 10006742), (18, 10006743), (19, 10006744), (20, 10006745), (21, 10006746), (22, 10006747), (23, 10006748), (24, 10006749), (25, 10006750), (26, 10006751), (27, 10006752), (28, 10006753), (29, 10006754), (30, 10006755), (31, 10006756), (32, 10006757), (33, 10006758), (34, 10006759), (35, 10006760), (36, 10006761), (37, 10006762), (38, 10006763), (39, 10006764), (40, 10006765), (41, 10006766), (42, 10006767), (43, 10006768), (44, 10006769), (45, 10006770), (46, 10006771), (47, 10006772), (48, 10006773), (49, 10006774), (50, 10006775), (51, 10006776), (52, 10006777), (53, 10006778), (54, 10006779), (55, 10006780), (56, 10006781), (57, 10006782), (58, 10006783), (59, 10006784), (60, 10006785), (61, 10006786), (62, 10006787), (63, 10006788), (64, 10006789), (65, 10006790), (66, 10006791), (67, 10006792), (68, 10006793), (69, 10006794), (70, 10006795), (71, 10006796), (72, 10006797), (73, 10006798), (74, 10006799), (75, 10006800), (76, 10006801), (77, 10006802), (78, 10006803), (79, 10006804), (80, 10006805), (81, 10006806), (82, 10006807), (83, 10006808), (84, 10006809), (85, 10006810), (86, 10006811), (87, 10006812), (88, 10006813), (89, 10006814), (90, 10006815), (91, 10006816), (92, 10006817), (93, 10006818), (94, 10006819), (95, 10006820), (96, 10006821), (97, 10006822), (98, 10006823), (99, 10006824), (100, 10006825)]\r\n```\r\n\r\nThe docs don't seem to give any indication of what the semantics are either way, so it might be good to clarify this on the docs.\r\n\r\nThanks,\r\n\r\nTim"}}