Initial commit


Former-commit-id: 8e17b2575f7f84095408b540f94c5033bca9ae1a
	modified:   denovogear-code/README.txt


Former-commit-id: b0c3ae08fa210c6261c01e04e9a6ec7a0feb39ca
modified readme


Former-commit-id: 5d5722a6054a855745553c7676ca0799a8495b43
Added BCF Parser and INDEL DNM Detection


Former-commit-id: e082117c73024598b34d4c08fa37097ed8262d3c [formerly 84bd392a5088dc92411fb46cfa4ac6604d2efc47]
Former-commit-id: 92e78dac0bfa4ac7e8c23b3dd5abf5a80ddf33b7
cleanup


Former-commit-id: d9c9492883e0ff06616f161504c510cb2dbdeae6 [formerly efb731200619451169dd555c187cf22c88fa2adc]
Former-commit-id: 1ea383f88081acb03cbba55fe36fbeddc4e79018
output ALT, updated README


Former-commit-id: c75fd813b8b485f117106b7c725e909e12aadcc2 [formerly 6f6a0433e8133da703808baec4f3cc51ce8f84ab]
Former-commit-id: bb4065fc12556ccc73f72098c934c4cc1585fe8b
Merge branch 'master' of ssh://git.code.sf.net/p/denovogear/code


Former-commit-id: e0486e350cf7b834a7bbd9bc9e27bec4664008dd [formerly 4f12a5dbfc6e8c9ec2116aadcce82207abbb047d]
Former-commit-id: 2f8b4f90d7b35d1f6957c7f516e6e68e2d6a91ba
variable mu based on indel lengths, internal lookup table generation, modified lookup table,  cmd line parameters


Former-commit-id: de99d7c5383ea61f6d8c86d80c20176124bb068f [formerly dd0c9b282da798c1fcee1ddbbf49100527915fe6]
Former-commit-id: 4a053ca1357f5d9ab2c4560a20391cdb1d668e07
cleanup


Former-commit-id: 716f229fb1006984b20483929283b321ddfacde4 [formerly 9cfe28e065e4a0ec2c64296d1751a164b2e7f97d]
Former-commit-id: b70eb54f58ec99dc8daee9fd76f17b33a728b4bd
cleanup


Former-commit-id: 617150727538b266304eaf078d9b627ede5777af [formerly cb185918e5d1b229ca20182976006bda31cd882d]
Former-commit-id: 6b272374291e7880048856b81c367d93540ba419
paired sample DNG detection


Former-commit-id: 0e97e1b0c385b02daeaa86c4d7ac541d30f6ffe6 [formerly 0a4a94176f7d305848a4533fa8b7fb6849a40efd]
Former-commit-id: c52164b152f039f328f6cbeaee67329941729c1b
updated pair-lookup


Former-commit-id: 64c25e6d9c7e492a9ecabeaebde67d9ecfa818ca [formerly 9563491fad777bfdaf92a64d2af22d9f4e678feb]
Former-commit-id: bf883ccefc8c80ed85c057f76f8fbf920f9c21e8
started phasing, not complete


Former-commit-id: 5ae7cf6fa3509c622df3720968fc67c4fc04a9ea [formerly b73355977f5038ddd822bde19024a286a2a3d4a9]
Former-commit-id: ae59d4242bb032ab0061a97e21d7dc1ffe7293be
parental phasing p2


Former-commit-id: 9c1c1203fd75ab76b8e82d831f3915d7cc259d47 [formerly 8eee13a602f7584fe2991ecf34f351b43f19642f]
Former-commit-id: b7c9d267ee6629abfe299045a1ab1cc0e14a840a
phasing cleanup


Former-commit-id: f3fe31e39f0a9b26fbb87baf3fd19647a5858cc8 [formerly a8c9280c00b4d96d88a078477cf08070535e79df]
Former-commit-id: a5dde2264fe7c5435ca65f77a4c01074c4a2afde
cleanup


Former-commit-id: 70ef5ed81515ff767b1cce77c435946ecc02da18 [formerly e98d7d23ae6a49a4ec622b909e6e257b481f7109]
Former-commit-id: ff82260c0123bb94084fff157d835d436c04b76b
phaser cleanup


Former-commit-id: 8d12b505d79f01cb823a6f4bf5b9e520578cb0e9 [formerly 8b577a2a2b89a07d662986e385317630e44a9f94]
Former-commit-id: 95a89fe5346d23a65158cae2c44e68d9e6158e19
cleanup phaser


Former-commit-id: 09b29ef62c8fcbf302b3e97883074776cbd9f859 [formerly 2a1a71419787ab0516cd6399d1dabe7b7e324865]
Former-commit-id: 27af96a4e8ba792436dd48996cf5d861938a890a
phaser- cleanup, reads gt3 in pgt_f, reads inh & var in dnm_f


Former-commit-id: 9f62a11b61acebdd11d1a7060d1e04be2376aa84 [formerly 9b0c9b0c700d855facec6fb4b2125429cc64f15a]
Former-commit-id: e96644fda51a619f539b3a59853d9f0f303833f5
remove lookup file creation


Former-commit-id: 7a8979c2e5f927a07d444c64cdf034d796f7b075 [formerly db08fcb3b27e19bb88e63a535d6dde34dc5e49c5]
Former-commit-id: a9ceedb9f7495e9f63310f68766bfd6feb9b2a7c