Issue in Common: Memory Leak in check_open_r (not closing file) #258
Description
Command to Verify
valgrind --leak-check=full \
--show-leak-kinds=all \
--track-origins=yes \
--verbose \
./hts_SuperDeduper/hts_SuperDeduper -T ../regression/hts_SuperDeduper.tab6
Output from Valgrind
==44234== HEAP SUMMARY:
==44234== in use at exit: 472 bytes in 1 blocks
==44234== total heap usage: 1,976 allocs, 1,975 frees, 291,733 bytes allocated
==44234==
==44234== Searching for pointers to 1 not-freed blocks
==44234== Checked 190,608 bytes
==44234==
==44234== 472 bytes in 1 blocks are still reachable in loss record 1 of 1
==44234== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==44234== by 0x4BC164D: __fopen_internal (iofopen.c:65)
==44234== by 0x4BC164D: fopen@@GLIBC_2.2.5 (iofopen.c:86)
==44234== by 0x1ED746: check_open_r(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) (in /home/david/Projects/HTStream/build/hts_SuperDeduper/hts_SuperDeduper)
==44234== by 0x1CC935: MainTemplate<SuperDeduperCounters, SuperDeduper>::main_func(int, char**) (in /home/david/Projects/HTStream/build/hts_SuperDeduper/hts_SuperDeduper)
==44234== by 0x1C0D7C: main (in /home/david/Projects/HTStream/build/hts_SuperDeduper/hts_SuperDeduper)
==44234==
==44234== LEAK SUMMARY:
==44234== definitely lost: 0 bytes in 0 blocks
==44234== indirectly lost: 0 bytes in 0 blocks
==44234== possibly lost: 0 bytes in 0 blocks
==44234== still reachable: 472 bytes in 1 blocks
==44234== suppressed: 0 bytes in 0 blocks
==44234==
==44234== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)
We need to ensure we don't leave the file pointer open.