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DEploid-dev / DEploid

dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infection setting.
http://deploid.readthedocs.io/en/latest/index.html
GNU General Public License v3.0
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travis osx valgrind memory check fails #154

Closed shajoezhu closed 8 years ago

shajoezhu commented 8 years ago 
 dEploid  --9950-- run: /usr/bin/dsymutil "./dEploid"
warning: no debug symbols in executable (-arch x86_64)
 done.
 dEploid -help --9955-- UNKNOWN mach_msg unhandled MACH_SEND_TRAILER option
--9955-- UNKNOWN mach_msg unhandled MACH_SEND_TRAILER option (repeated 2 times)
--9955-- UNKNOWN mach_msg unhandled MACH_SEND_TRAILER option (repeated 4 times)
==9955== 40 bytes in 1 blocks are definitely lost in loss record 30 of 86
==9955==    at 0x100048ABB: malloc (in /usr/local/Cellar/valgrind/3.11.0_1/lib/valgrind/vgpreload_memcheck-amd64-darwin.so)
==9955==    by 0x1005FDC9E: _object_remove_assocations (in /usr/lib/libobjc.A.dylib)
==9955==    by 0x1005F7DB7: objc_destructInstance (in /usr/lib/libobjc.A.dylib)
==9955==    by 0x1005F7D0C: object_dispose (in /usr/lib/libobjc.A.dylib)
==9955==    by 0x1005ABD68: -[OS_xpc_object _xref_dispose] (in /usr/lib/system/libxpc.dylib)
==9955==    by 0x1005ACCC9: xpc_pipe_routine (in /usr/lib/system/libxpc.dylib)
==9955==    by 0x1005AC9DD: _xpc_interface_routine (in /usr/lib/system/libxpc.dylib)
==9955==    by 0x1005AC5C3: bootstrap_look_up3 (in /usr/lib/system/libxpc.dylib)
==9955==    by 0x1005AC4F8: bootstrap_look_up2 (in /usr/lib/system/libxpc.dylib)
==9955==    by 0x100533907: ___notify_lib_init_block_invoke (in /usr/lib/system/libsystem_notify.dylib)
==9955==    by 0x1001F740A: _dispatch_client_callout (in /usr/lib/system/libdispatch.dylib)
==9955==    by 0x1001F7302: dispatch_once_f (in /usr/lib/system/libdispatch.dylib)
==9955== 
==9955== 56 bytes in 1 blocks are definitely lost in loss record 35 of 86
==9955==    at 0x100048ABB: malloc (in /usr/local/Cellar/valgrind/3.11.0_1/lib/valgrind/vgpreload_memcheck-amd64-darwin.so)
==9955==    by 0x100300802: localtime (in /usr/lib/system/libsystem_c.dylib)
==9955==    by 0x1003009C6: ctime (in /usr/lib/system/libsystem_c.dylib)
==9955==    by 0x10000CF26: DEploidIO::getTime(bool) (in ./dEploid)
==9955==    by 0x10000AB9F: DEploidIO::DEploidIO(int, char**) (in ./dEploid)
==9955==    by 0x100000CA8: main (in ./dEploid)
==9955== 
==9955== 104 (56 direct, 48 indirect) bytes in 1 blocks are definitely lost in loss record 53 of 86
==9955==    at 0x1000491B9: calloc (in /usr/local/Cellar/valgrind/3.11.0_1/lib/valgrind/vgpreload_memcheck-amd64-darwin.so)
==9955==    by 0x1005F759B: _objc_fetch_pthread_data (in /usr/lib/libobjc.A.dylib)
==9955==    by 0x1005F7500: _fetchInitializingClassList(signed char) (in /usr/lib/libobjc.A.dylib)
==9955==    by 0x1005F71A5: _class_initialize (in /usr/lib/libobjc.A.dylib)
==9955==    by 0x1005F7122: _class_initialize (in /usr/lib/libobjc.A.dylib)
==9955==    by 0x1005F7122: _class_initialize (in /usr/lib/libobjc.A.dylib)
==9955==    by 0x1005F7122: _class_initialize (in /usr/lib/libobjc.A.dylib)
==9955==    by 0x1005F6C8F: lookUpImpOrForward (in /usr/lib/libobjc.A.dylib)
==9955==    by 0x1005F0590: objc_msgSend (in /usr/lib/libobjc.A.dylib)
==9955==    by 0x1005ACCC9: xpc_pipe_routine (in /usr/lib/system/libxpc.dylib)
==9955==    by 0x1005AC9DD: _xpc_interface_routine (in /usr/lib/system/libxpc.dylib)
==9955==    by 0x1005AC5C3: bootstrap_look_up3 (in /usr/lib/system/libxpc.dylib)
==9955==