GitHub PushEvent at 2014-08-22 15:17:36
Repository: bwa
Actor: nh13
Payload: {"shas":[["cffff4338fcf1b7458bf8c3c3ac9dbb3067b3e63","1c4d00be5dc5190a134a33148b421d0ebd469860@me.com","r787: use mem_seed_sw() also for non-PacBio reads\n\nIn the previous version, mem_seed_sw() is only used for PacBio reads to filter\nbad seeds. For non-PacBio long queries, bwa-mem uses mem_chain2aln_short() for\na similar purpose. However, it turns out that mem_chain2aln_short() is not\neffective given long near-tandem repeats. Bwa-mem still wastes a lot of time\nof futile ref substring and extensions.\n\nIn this commit, mem_chain2aln_short() has been removed. mem_seed_sw() is used\nif the query sequence is long enough (~700bp). For shorter reads, the results\nshould be almost identical to the previous version.","Heng Li",false],["7fd6a11569f84540642071e3c4f39068d586fdbc","1c4d00be5dc5190a134a33148b421d0ebd469860@me.com","r788: segfault when the last ref is \"weird\"\n\nmem_patch_reg() did not check if two hits are on the same strand, which may\nlead to an alignment bridging the forward-backward boundary.","Heng Li",false],["705aa538947a0681de575f0f0d5c65593f80cf14","1c4d00be5dc5190a134a33148b421d0ebd469860@me.com","Released 0.7.10","Heng Li",false],["482a47a57ed9aa203387d417f898efe57502f313","1348f174e6aba549c3457e87ad1ee4ecf75c6292@broadinstitute.org","adding support for SAM/BAM output using htslib.  Please turn on within\nthe Makefile.","Nils Homer",false],["5e56bec0f4461420af8162ad57d10871284b89e3","1c4d00be5dc5190a134a33148b421d0ebd469860@me.com","don't process hard clipped SEQ\n\nThe full read sequence has to be present.","Heng Li",false],["b5415ba23db40ea518e76d4d9e886469171295a6","1c4d00be5dc5190a134a33148b421d0ebd469860@me.com","first integration; compiled, but NOT TESTED!","Heng Li",false],["d9dfab2ba231fd918935dc0be9b726360516079b","1c4d00be5dc5190a134a33148b421d0ebd469860@me.com","r795: intel's ksw_extend() replacement","Heng Li",false],["a1a57d97be0f40b4d156cfff10df4db25ccb2cd9","1c4d00be5dc5190a134a33148b421d0ebd469860@me.com","r796: more debugging code","Heng Li",false],["9bdcf31dec41ed97a7bfc4ed9c4cfafe55e41dac","1c4d00be5dc5190a134a33148b421d0ebd469860@me.com","don't process hard clipped SEQ\n\nThe full read sequence has to be present.","Heng Li",false],["c1df343740e6be723429e674c2dcfd23fbc17cd1","33eb956fdce63120767e59150e1afb42ff32d549@sparkdmz1.spark0.intel.com","Merge branch 'master' of github.com:lh3/bwa","Mustafa Ozdal",false],["0a6f2660b42a223c95b98bad8b06e851b79e470e","33eb956fdce63120767e59150e1afb42ff32d549@sparkdmz1.spark0.intel.com","Fixed a bug related to the score returned.","Mustafa Ozdal",false],["b73f4c977a53c6b4a9a18c85bd4e6560cf80eb5b","1c4d00be5dc5190a134a33148b421d0ebd469860@me.com","Merge branch 'master' into new-master","Heng Li",false],["8a230db596b25e137a66df26f9b833dfd5add0b9","1c4d00be5dc5190a134a33148b421d0ebd469860@me.com","Merge branch 'nh_bam_support' of git://github.com/nh13/bwa into nh13-nh_bam_support","Heng Li",false],["1de61b556ee3bcb7b44a28b10b8c81a98dda35a2","1c4d00be5dc5190a134a33148b421d0ebd469860@me.com","r806: polish BAM support","Heng Li",false],["ec85997b7d56efd7459a7c81a4fe8066c1a8021d","1348f174e6aba549c3457e87ad1ee4ecf75c6292@broadinstitute.org","adding determinism to bwa mem by allowing the user to specify a fixed\nchunk size, rather than have it vary due to the number of threads.","Nils Homer",true]],"size":15,"ref":"refs/heads/nh_bwa_mem_determinism","head":"ec85997b7d56efd7459a7c81a4fe8066c1a8021d"}