segfault during hts_md5_update

[OctavioGalland]

Summary

Segfault in hts_md5_update during parsing of a crafted SAM/FASTA file pair.

Environment

Built using LLVM 14 with ASAN on Ubuntu 22.04

How to reproduce

Build with ASAN on latest commit like so:

git clone --recursive https://github.com/samtools/htslib
cd htslib
autoreconf -i
CC=clang-14 CXX=clang++-14 CFLAGS="-fsanitize=address -g" CXXFLAGS="-fsanitize=address -g" LDFLAGS="-fsanitize=address -g" ./configure
make -j$(nproc)

git clone --recursive https://github.com/samtools/samtools
cd samtools
autoheader
autoconf -Wno-syntax
CC=clang-14 CXX=clang++-14 CFLAGS="-fsanitize=address -g -I$(pwd)/../htslib" CXXFLAGS="-fsanitize=address -g -I$(pwd)/../htslib" LDFLAGS="-fsanitize=address -g -L$(pwd)/../htslib" ./configure
make -j$(nproc)

Within the samtools folder, get poc file and reproduce with:

echo -ne "QFNRCVNOOmMxCUxOOjEwCnMwCTAJYzEJMTAwMDAwMDAwMDAwCTAJKjAJQTFDQ0dDR0dUVDEJMgkw
CTENTQkqCTAqKkNDQ0NYUEP/ZEJDSEMqKgoqUQlTATpjMQlMTjoxMApzMAkwCWMxCTEJMAkqMAlB
MUNDR0NHR1RUGQkyCTAJMQ1NCSoKczAJMAljMQkxCTAJKjAJQTFDQ0dDR0dUVDEJMgkwCTFRCVNO
OmMxCUxOOjEwCnMwCTAJYzEJMQkwCSowCUExQ0NHQ0dHVFQZCTIJMCoqCg==" | base64 -d > poc
./samtools view -C -T ../htslib/test/c2.fa poc

Which on my setup outputs:

[W::cram_get_ref] Reference file given, but ref 'c1' not present
[W::cram_get_ref] Failed to populate reference for id 0
[W::cram_write_SAM_hdr] No M5 tags present and could not find reference
[W::cram_write_SAM_hdr] Enabling embed_ref=2 option
[W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference
CRAM-�\��vvr@SQ	SN:c1	LN:10
@PG	ID:samtools	PN:samtools	VN:1.18-21-g528e1b2	CL:./samtools view -C -T ../htslib/test/c2.fa poc
�	�??}�Y�[W::sam_parse1] mapped query must have a CIGAR; treated as unmapped
[W::sam_parse1] unrecognized mate reference name "A1CCGCGGTT1"; treated as unmapped
[W::sam_read1_sam] Parse error at line 3
AddressSanitizer:DEADLYSIGNAL
=================================================================
==11502==ERROR: AddressSanitizer: SEGV on unknown address 0x61a700001980 (pc 0x7f43074c49bf bp 0x7ffca087c6c0 sp 0x7ffca087be88 T0)
==11502==The signal is caused by a READ memory access.
    #0 0x7f43074c49bf  string/../sysdeps/x86_64/multiarch/memmove-vec-unaligned-erms.S:370
    #1 0x559b356add81 in __asan_memcpy (/home/octavio/samtools/samtools+0x132d81) (BuildId: 7078ea94d4e08689f85e1df47e2d609c021d2440)
    #2 0x559b359c13e9 in hts_md5_update /home/octavio/htslib/md5.c:268:2
    #3 0x559b35a7fcbd in cram_encode_container /home/octavio/htslib/cram/cram_encode.c:2041:17
    #4 0x559b35aef96c in cram_flush_container /home/octavio/htslib/cram/cram_io.c:4128:14
    #5 0x559b35af0795 in cram_flush_container_mt /home/octavio/htslib/cram/cram_io.c:4280:16
    #6 0x559b35afb742 in cram_flush /home/octavio/htslib/cram/cram_io.c:5431:19
    #7 0x559b3598a2e7 in hts_flush /home/octavio/htslib/hts.c:1667:16
    #8 0x559b35903084 in vprint_error_core /home/octavio/samtools/sam_utils.c:48:26
    #9 0x559b3590345c in print_error_errno /home/octavio/samtools/sam_utils.c:71:5
    #10 0x559b3570c472 in stream_view /home/octavio/samtools/sam_view.c:762:9
    #11 0x559b35707be8 in main_samview /home/octavio/samtools/sam_view.c:1363:15
    #12 0x559b35786eed in main /home/octavio/samtools/bamtk.c:244:55
    #13 0x7f4307429d8f in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16
    #14 0x7f4307429e3f in __libc_start_main csu/../csu/libc-start.c:392:3
    #15 0x559b3562bb24 in _start (/home/octavio/samtools/samtools+0xb0b24) (BuildId: 7078ea94d4e08689f85e1df47e2d609c021d2440)

AddressSanitizer can not provide additional info.
SUMMARY: AddressSanitizer: SEGV string/../sysdeps/x86_64/multiarch/memmove-vec-unaligned-erms.S:370 
==11502==ABORTING