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            "Development Status :: 3 - Alpha",
            "License :: OSI Approved :: BSD License",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "Unique-Sam\n==========\n\n**Unique-Sam** is a simple command line tool to remove the duplicated\nalignments in the `SAM <https://github.com/samtools/hts-specs>`__ file.\nIf the MAPQ field of the alignment is available, *unique-sam* will keep\none and only one alignment with the highest score. Otherwise,\n*unique-sam* will calculate a score according to the alignment's MD or\nCIGAR field and use the calculated value to remove the duplicated\nalignments.\n\nInstall\n=======\n\n-  Install with the source code, in the source folder:\n\n   .. code:: bash\n\n       python setup.py install\n\n-  If you have `**pip** <https://pip.pypa.io/en/latest/index.html>`__\n   installed, you can simply run\n\n   .. code:: bash\n\n       pip install unique-sam\n\n   After installation you can access **unique-sam** from your command\n   line.\n\nUsage\n=====\n\n**unique-sam** need a SAM format file to run properly. Before using\n``unique-sam`` command, we must sort the sam file by the\n``QNAME``\\ field. You can use ``samtools`` to achieve this purpose,\nrefer to samtools for more helps:\n\n.. code:: bash\n\n    samtools sort --help\n\nFor basic usage, in your command line environment:\n\n.. code:: bash\n\n    unique-sam input.sam -o output.sam\n\n-s Parameter\n~~~~~~~~~~~~\n\nIf you don't have access to samtools, you can use **-s** option of\n``unique-sam``:\n\n.. code:: shell\n\n    unique-sam -s input.sam -o output.sam\n\nThe sort functionality of ``unique-sam`` is implemented as\n\n1. copy a temp file from the original sam file\n2. extract the header of the sam file\n3. sort the alignments with Bash ``sort`` program\n\n-k Parameter\n~~~~~~~~~~~~\n\n``-k`` parameter give you the control on how to extract the alignment\nkey from qname field the parameter of the ``-k`` is a regular\nexpression. You should group the key part with parentheses. \\*\\* e.g.\n1\\*\\* > qname:\n``N|GACGCGGATCTT/500407:4:H03E5AFXX:1:21109:5977:6969_2:N:0:ATACAA`` > >\n``-k '(.*)\\_[1-2](.*)'`` > > key will be:\n``N|GACGCGGATCTT/500407:4:H03E5AFXX:1:21109:5977:6969:N:0:ATACAA`` >\nwhich will remove the ``_1/2`` part of the qname.\n\n\\*\\* e.g. 2\\*\\* > qname: ``HWI-ST667_0147:1:1101:1128:2079#CGATGT/1`` >\n> ``-k '(.*)\\/[1-2]'`` > > key will be:\n``HWI-ST667_0147:1:1101:1128:2079#CGATGT`` > which will remove the\n``/1/2`` part of the qname.\n\nFor more about **unique-sam** run:\n\n.. code:: bash\n\n    unique-sam --help\n\nUnique Strategy\n===============\n\nFollowing strategies are applied to find the unique & the best alignment\n\n1. Keep the alignment pair that has the highest score. If more than one\n   pairs are found to have the same \"Highest Score\", these pairs will be\n   removed.\n2. Read1 and Read2 should be mapped on different strands.\n3. The segment length decided by the read pairs should be longer than\n   0.7 \\* read length\n\nLog File\n========\n\nAll removed alignments will be written into log file ``input.sam.log``\nunder current folder. Each line of the log file start with a symbol and\nfollowed by the deleted alignment (the original alignment record in the\n``input.sam``). The symbol describe the reason of why this/these\nalignments should be removed. The specification of these symbols are\nlisted in the follow table:\n\n\\| Symbol \\| Description \\| \\| ------ \\| ----------- \\| \\| **!** \\|\nError lines \\| \\| **<** \\| Low score alignments \\| \\| **=** \\| Pairs\nwith more than one best score \\| \\| **~** \\| Read pair mapped on the\nsame strand \\| \\| **?** \\| Segment length too short \\| \\| **-** \\|\nInvalid read1/2 information in flag filed or unmapped segment \\|\n\nCopyright\n=========\n\nCopyright (c) 2015 dlmeduLi@163.com",
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