SAM tools Files

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htslib - changes v1.22.1
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Bug Fixes
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* SECURITY fix: Prevent CRAM byte_array decoder from overflowing its output
  buffer.  This could be triggered by certain malformed CRAM inputs.
  (PR #1934)

* Two fixes for crashes reported when trying to save data with very long
  alignment records with sequence '*' as CRAM 3.1:

  - The htscodecs submodule is updated to v1.6.4. This includes a fix to the
    rANS encoder to prevent it from failing on these inputs.
    (PR #1935.  Reported by Martin Pollard)

  - Improved error handling in cram_compress_block2().  If the
    previously-chosen CRAM compression method starts to fail, it will now
    try other methods instead of giving up immediately.
    (PR #1931.  Reported by Martin Pollard)

* Fix warnings due to the wrong datatype being passed to curl_easy_setopt()
  (PR #1925.  Thanks to John Marshall)

* Prevent instances of `memcpy(out, NULL, 0)`, which is strictly undefined
  behaviour.
  (PR #1930.  Thanks to Ben Lawrence).

Build Changes
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* Fixed compilation against older glibc / macOS SDKs that incorrectly
  suppressed some symbols if _XOPEN_SOURCE was defined.
  (PR #1928.  Reported by John Marshall)

* Fixed ref-cache configure check for libcurl, so that if libcurl is not
  available, or turned off by `./configure --disable-libcurl`, the
  `ref-cache` build will be automatically disabled as well.
  (PR #1929, fixes #1926.  Reported by biounix)

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samtools - changes v1.22.1
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Bug fixes:

* SECURITY: Fix use-after-free bug in `samtools mpileup -a` due to reference
  sequences being discarded too early.  This could happen when the `-a`
  option was used, and all the alignments for one of the references started
  at the same position.  This caused mpileup to try to load the next
  reference before it had finished writing data for the previous one out.
  (PR #2229, fixes #2227.  Reported by Pouya Kheradpour)

* This release bundles htslib-1.22.1 and htscodecs v1.6.4.  Fixes a possible
  buffer overflow on some invalid CRAM inputs; and a failure when trying to
  save data with very long alignment records with sequence '*' as CRAM
  version 3.1.

  See the HTSlib and htscodecs NEWS files for details.

Documentation:

* Clarify that `-@` starts additional threads in `samtools index` help, and
  fix formatting issues in the `samtools reset` manual page.
  (PR #2225)

Build changes:

* Added settings to limit memory used by `samtools sort` when running tests.
  (PR #2226)