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Fix warnings #4

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Fix warnings #4

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@donald donald commented Oct 7, 2017

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This file had some lines terminated with "\r\n" and
others with "\n" only, which most editors don't like.

Convert to "\n" line endings.
No functional change intended.

Various fixes to prevent warnings.

In fact, we are clean now for

    make CXXFLAGS="-Wall -Werror"

But only because "-Wall" will not be propagated
to the subdirectories...
donald added a commit that referenced this pull request Oct 9, 2017
This fixed size array, which overflows when more than 64 threads
are requested, is not used. Remove it.

Bug identified by address sanitizer:

    #0 0x449813 in Do_PairAlign() /scratch/cluster/buczek/bsmap/bsmap.git/main.cpp:129
    #1 0x4527e4 in RunProcess() /scratch/cluster/buczek/bsmap/bsmap.git/main.cpp:498
    #2 0x40613c in main /scratch/cluster/buczek/bsmap/bsmap.git/main.cpp:609
    #3 0x7f0dff71803f in __libc_start_main ../csu/libc-start.c:308
    #4 0x40a0c9 in _start (/scratch/cluster02/buczek/bsmap/bsmap.git/bsmap+0x40a0c9)

    0x00000069b9e0 is located 32 bytes to the left of global variable 'read_time' defined in 'main.cpp:45:19' (0x69ba00) of size 4
    0x00000069b9e0 is located 0 bytes to the right of global variable 'tid' defined in 'main.cpp:46:9' (0x69b960) of size 128
    SUMMARY: AddressSanitizer: global-buffer-overflow /scratch/cluster/buczek/bsmap/bsmap.git/main.cpp:129 in Do_PairAlign()
    Shadow bytes around the buggy address:
      0x0000800cb6e0: 00 00 00 00 00 f9 f9 f9 f9 f9 f9 f9 00 00 00 00
      0x0000800cb6f0: 00 f9 f9 f9 f9 f9 f9 f9 00 00 00 00 00 00 00 00
      0x0000800cb700: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
      0x0000800cb710: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
      0x0000800cb720: 00 00 00 00 00 00 00 f9 f9 f9 f9 f9 00 00 00 00
    =>0x0000800cb730: 00 00 00 00 00 00 00 00 00 00 00 00[f9]f9 f9 f9
      0x0000800cb740: 04 f9 f9 f9 f9 f9 f9 f9 04 f9 f9 f9 f9 f9 f9 f9
      0x0000800cb750: 04 f9 f9 f9 f9 f9 f9 f9 04 f9 f9 f9 f9 f9 f9 f9
      0x0000800cb760: 04 f9 f9 f9 f9 f9 f9 f9 04 f9 f9 f9 f9 f9 f9 f9
      0x0000800cb770: 04 f9 f9 f9 f9 f9 f9 f9 04 f9 f9 f9 f9 f9 f9 f9
      0x0000800cb780: 04 f9 f9 f9 f9 f9 f9 f9 04 f9 f9 f9 f9 f9 f9 f9
    Shadow byte legend (one shadow byte represents 8 application bytes):
      Addressable:           00
      Partially addressable: 01 02 03 04 05 06 07
      Heap left redzone:       fa
      Freed heap region:       fd
      Stack left redzone:      f1
      Stack mid redzone:       f2
      Stack right redzone:     f3
      Stack after return:      f5
      Stack use after scope:   f8
      Global redzone:          f9
      Global init order:       f6
      Poisoned by user:        f7
      Container overflow:      fc
      Array cookie:            ac
      Intra object redzone:    bb
      ASan internal:           fe
      Left alloca redzone:     ca
      Right alloca redzone:    cb
    ==6441==ABORTING
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