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Fix problems with older PHP versions

Fokkema requested to merge fix/PHP_versions into master

Fixes some problems existing in older PHP versions (PHP < 5.4.0). We won't officially support PHP versions below 5.4.0, but as long as it's a simple change to help a users, we can make those changes.

  • mm10_transcript_positions_create.php:
    • Updated preg_match_all() call to be compatible with PHP versions < 5.4.0.
  • get_read_length_per_gene.php, mm10_transcript_positions_create.php, packed_sam2wiggle.php:
    • Added link to inc-lib-json.php to be compatible with PHP versions < 5.2.0.
    • The code in inc-lib-json.php is taken, with permission, from gajendrakrjain.wordpress.com.
  • Updated readme to mention minimal required PHP version (5.4), and made a small speed improvement to a bash command there.

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