build index (memory allocation issue)

[erivals]

Hi Agnieszka
after your last commit i ran a larger test with a few variants and build crashed because of memory allocation issue. I got the same for distinct parameters
I'll send you the fasta and vcf files per email.
best
E.
Below the command and console message:

MuGI_build rCRS-MT.fa mini-VT.vcf 15 3 1
Reference sequence: rCRS-MT.fa
Compressing reference sequence...
Reference sequence compressed and written to the output file.
VCF file: mini-VT.vcf
There are 13 variant calls for 10 haploid individuals.
Creating a dictionary file.
Processing VCF data... 
Processed 100% of the input vcf
Compressing variant list... 
*** Error in `MuGI_build': double free or corruption (!prev): 0x00000000010a92e0 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f2fc3afc7e5]
/lib/x86_64-linux-gnu/libc.so.6(+0x8037a)[0x7f2fc3b0537a]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7f2fc3b0953c]
MuGI_build[0x40fdd6]
MuGI_build[0x4032ea]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f2fc3aa5830]
MuGI_build[0x403d99]
======= Memory map: ========
00400000-00421000 r-xp 00000000 fd:00 7637351                            /home/rivals/local/MuGI/MuGI_build
00620000-00621000 r--p 00020000 fd:00 7637351                            /home/rivals/local/MuGI/MuGI_build
00621000-00622000 rw-p 00021000 fd:00 7637351                            /home/rivals/local/MuGI/MuGI_build
0108c000-01acc000 rw-p 00000000 00:00 0                                  [heap]
7f2fbc000000-7f2fbc021000 rw-p 00000000 00:00 0 
7f2fbc021000-7f2fc0000000 ---p 00000000 00:00 0 
7f2fc1937000-7f2fc1938000 ---p 00000000 00:00 0 
7f2fc1938000-7f2fc2138000 rw-p 00000000 00:00 0 
7f2fc2138000-7f2fc2139000 ---p 00000000 00:00 0 
7f2fc2139000-7f2fc2939000 rw-p 00000000 00:00 0 
7f2fc2939000-7f2fc293a000 ---p 00000000 00:00 0 
7f2fc293a000-7f2fc333a000 rw-p 00000000 00:00 0 
7f2fc333a000-7f2fc3353000 r-xp 00000000 fd:00 12988892                   /usr/lib/x86_64-linux-gnu/libtbbmalloc.so.2
7f2fc3353000-7f2fc3552000 ---p 00019000 fd:00 12988892                   /usr/lib/x86_64-linux-gnu/libtbbmalloc.so.2
7f2fc3552000-7f2fc3553000 r--p 00018000 fd:00 12988892                   /usr/lib/x86_64-linux-gnu/libtbbmalloc.so.2
7f2fc3553000-7f2fc3555000 rw-p 00019000 fd:00 12988892                   /usr/lib/x86_64-linux-gnu/libtbbmalloc.so.2
7f2fc3555000-7f2fc3578000 rw-p 00000000 00:00 0 
7f2fc3578000-7f2fc3680000 r-xp 00000000 fd:00 12715702                   /lib/x86_64-linux-gnu/libm-2.23.so
7f2fc3680000-7f2fc387f000 ---p 00108000 fd:00 12715702                   /lib/x86_64-linux-gnu/libm-2.23.so
7f2fc387f000-7f2fc3880000 r--p 00107000 fd:00 12715702                   /lib/x86_64-linux-gnu/libm-2.23.so
7f2fc3880000-7f2fc3881000 rw-p 00108000 fd:00 12715702                   /lib/x86_64-linux-gnu/libm-2.23.so
7f2fc3881000-7f2fc3884000 r-xp 00000000 fd:00 12715659                   /lib/x86_64-linux-gnu/libdl-2.23.so
7f2fc3884000-7f2fc3a83000 ---p 00003000 fd:00 12715659                   /lib/x86_64-linux-gnu/libdl-2.23.so
7f2fc3a83000-7f2fc3a84000 r--p 00002000 fd:00 12715659                   /lib/x86_64-linux-gnu/libdl-2.23.so
7f2fc3a84000-7f2fc3a85000 rw-p 00003000 fd:00 12715659                   /lib/x86_64-linux-gnu/libdl-2.23.so
7f2fc3a85000-7f2fc3c45000 r-xp 00000000 fd:00 12715695                   /lib/x86_64-linux-gnu/libc-2.23.so
7f2fc3c45000-7f2fc3e45000 ---p 001c0000 fd:00 12715695                   /lib/x86_64-linux-gnu/libc-2.23.so
7f2fc3e45000-7f2fc3e49000 r--p 001c0000 fd:00 12715695                   /lib/x86_64-linux-gnu/libc-2.23.so
7f2fc3e49000-7f2fc3e4b000 rw-p 001c4000 fd:00 12715695                   /lib/x86_64-linux-gnu/libc-2.23.so
7f2fc3e4b000-7f2fc3e4f000 rw-p 00000000 00:00 0 
7f2fc3e4f000-7f2fc3e67000 r-xp 00000000 fd:00 12715672                   /lib/x86_64-linux-gnu/libpthread-2.23.so
7f2fc3e67000-7f2fc4066000 ---p 00018000 fd:00 12715672                   /lib/x86_64-linux-gnu/libpthread-2.23.so
7f2fc4066000-7f2fc4067000 r--p 00017000 fd:00 12715672                   /lib/x86_64-linux-gnu/libpthread-2.23.so
7f2fc4067000-7f2fc4068000 rw-p 00018000 fd:00 12715672                   /lib/x86_64-linux-gnu/libpthread-2.23.so
7f2fc4068000-7f2fc406c000 rw-p 00000000 00:00 0 
7f2fc406c000-7f2fc4082000 r-xp 00000000 fd:00 12718490                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7f2fc4082000-7f2fc4281000 ---p 00016000 fd:00 12718490                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7f2fc4281000-7f2fc4282000 rw-p 00015000 fd:00 12718490                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7f2fc4282000-7f2fc42a3000 r-xp 00000000 fd:00 12976810                   /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f2fc42a3000-7f2fc44a2000 ---p 00021000 fd:00 12976810                   /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f2fc44a2000-7f2fc44a3000 r--p 00020000 fd:00 12976810                   /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f2fc44a3000-7f2fc44a4000 rw-p 00021000 fd:00 12976810                   /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f2fc44a4000-7f2fc4616000 r-xp 00000000 fd:00 12976687                   /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f2fc4616000-7f2fc4816000 ---p 00172000 fd:00 12976687                   /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f2fc4816000-7f2fc4820000 r--p 00172000 fd:00 12976687                   /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f2fc4820000-7f2fc4822000 rw-p 0017c000 fd:00 12976687                   /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f2fc4822000-7f2fc4826000 rw-p 00000000 00:00 0 
7f2fc4826000-7f2fc485d000 r-xp 00000000 fd:00 12988894                   /usr/lib/x86_64-linux-gnu/libtbb.so.2
7f2fc485d000-7f2fc4a5d000 ---p 00037000 fd:00 12988894                   /usr/lib/x86_64-linux-gnu/libtbb.so.2
7f2fc4a5d000-7f2fc4a5e000 r--p 00037000 fd:00 12988894                   /usr/lib/x86_64-linux-gnu/libtbb.so.2
7f2fc4a5e000-7f2fc4a60000 rw-p 00038000 fd:00 12988894                   /usr/lib/x86_64-linux-gnu/libtbb.so.2
7f2fc4a60000-7f2fc4a63000 rw-p 00000000 00:00 0 
7f2fc4a63000-7f2fc4a89000 r-xp 00000000 fd:00 12715663                   /lib/x86_64-linux-gnu/ld-2.23.so
7f2fc4c5a000-7f2fc4c62000 rw-p 00000000 00:00 0 
7f2fc4c67000-7f2fc4c88000 rw-p 00000000 00:00 0 
7f2fc4c88000-7f2fc4c89000 r--p 00025000 fd:00 12715663                   /lib/x86_64-linux-gnu/ld-2.23.so
7f2fc4c89000-7f2fc4c8a000 rw-p 00026000 fd:00 12715663                   /lib/x86_64-linux-gnu/ld-2.23.so
7f2fc4c8a000-7f2fc4c8b000 rw-p 00000000 00:00 0 
7ffcd418a000-7ffcd4284000 rw-p 00000000 00:00 0                          [stack]
7ffcd436c000-7ffcd436f000 r--p 00000000 00:00 0                          [vvar]
7ffcd436f000-7ffcd4371000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
Abandon