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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "https://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en-US">
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<title>btllib: btllib Namespace Reference</title>
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<div id="doc-content">
<div class="header">
<div class="summary">
<a href="#nested-classes">Classes</a> |
<a href="#typedef-members">Typedefs</a> |
<a href="#func-members">Functions</a> |
<a href="#var-members">Variables</a> </div>
<div class="headertitle"><div class="title">btllib Namespace Reference</div></div>
</div><!--header-->
<div class="contents">
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="nested-classes" name="nested-classes"></a>
Classes</h2></td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="classbtllib_1_1AAHash.html">AAHash</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="classbtllib_1_1BlindNtHash.html">BlindNtHash</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="classbtllib_1_1BlindSeedNtHash.html">BlindSeedNtHash</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="classbtllib_1_1BloomFilter.html">BloomFilter</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="classbtllib_1_1CountingBloomFilter.html">CountingBloomFilter</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="classbtllib_1_1Indexlr.html">Indexlr</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="classbtllib_1_1KmerBloomFilter.html">KmerBloomFilter</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="classbtllib_1_1KmerCountingBloomFilter.html">KmerCountingBloomFilter</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="classbtllib_1_1NtHash.html">NtHash</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="classbtllib_1_1ProcessPipeline.html">ProcessPipeline</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="classbtllib_1_1RandSeq.html">RandSeq</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="classbtllib_1_1SeedAAHash.html">SeedAAHash</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="classbtllib_1_1SeedBloomFilter.html">SeedBloomFilter</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="classbtllib_1_1SeedNtHash.html">SeedNtHash</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="classbtllib_1_1SeqReader.html">SeqReader</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="classbtllib_1_1SeqWriter.html">SeqWriter</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="typedef-members" name="typedef-members"></a>
Typedefs</h2></td></tr>
<tr class="memitem:ad25389c5fa412fe5932440b799de27bc" id="r_ad25389c5fa412fe5932440b799de27bc"><td class="memItemLeft" align="right" valign="top"><a id="ad25389c5fa412fe5932440b799de27bc" name="ad25389c5fa412fe5932440b799de27bc"></a>
using </td><td class="memItemRight" valign="bottom"><b>SpacedSeed</b> = std::vector<unsigned></td></tr>
<tr class="separator:ad25389c5fa412fe5932440b799de27bc"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0facae882d851c781ed73f248dd76166" id="r_a0facae882d851c781ed73f248dd76166"><td class="memItemLeft" align="right" valign="top"><a id="a0facae882d851c781ed73f248dd76166" name="a0facae882d851c781ed73f248dd76166"></a>
using </td><td class="memItemRight" valign="bottom"><b>CountingBloomFilter8</b> = <a class="el" href="classbtllib_1_1CountingBloomFilter.html">CountingBloomFilter</a><uint8_t></td></tr>
<tr class="separator:a0facae882d851c781ed73f248dd76166"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9268f52ac6a44f9a31da9c1e5b0e2514" id="r_a9268f52ac6a44f9a31da9c1e5b0e2514"><td class="memItemLeft" align="right" valign="top"><a id="a9268f52ac6a44f9a31da9c1e5b0e2514" name="a9268f52ac6a44f9a31da9c1e5b0e2514"></a>
using </td><td class="memItemRight" valign="bottom"><b>CountingBloomFilter16</b> = <a class="el" href="classbtllib_1_1CountingBloomFilter.html">CountingBloomFilter</a><uint16_t></td></tr>
<tr class="separator:a9268f52ac6a44f9a31da9c1e5b0e2514"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:acd56289187ad730ba734321a0e0c0a8d" id="r_acd56289187ad730ba734321a0e0c0a8d"><td class="memItemLeft" align="right" valign="top"><a id="acd56289187ad730ba734321a0e0c0a8d" name="acd56289187ad730ba734321a0e0c0a8d"></a>
using </td><td class="memItemRight" valign="bottom"><b>CountingBloomFilter32</b> = <a class="el" href="classbtllib_1_1CountingBloomFilter.html">CountingBloomFilter</a><uint32_t></td></tr>
<tr class="separator:acd56289187ad730ba734321a0e0c0a8d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac7d568fa2bff881cb92fbd56b93cb730" id="r_ac7d568fa2bff881cb92fbd56b93cb730"><td class="memItemLeft" align="right" valign="top"><a id="ac7d568fa2bff881cb92fbd56b93cb730" name="ac7d568fa2bff881cb92fbd56b93cb730"></a>
using </td><td class="memItemRight" valign="bottom"><b>KmerCountingBloomFilter8</b> = <a class="el" href="classbtllib_1_1KmerCountingBloomFilter.html">KmerCountingBloomFilter</a><uint8_t></td></tr>
<tr class="separator:ac7d568fa2bff881cb92fbd56b93cb730"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a37cec0aa234dbc5f9eb174bf3dd6f11a" id="r_a37cec0aa234dbc5f9eb174bf3dd6f11a"><td class="memItemLeft" align="right" valign="top"><a id="a37cec0aa234dbc5f9eb174bf3dd6f11a" name="a37cec0aa234dbc5f9eb174bf3dd6f11a"></a>
using </td><td class="memItemRight" valign="bottom"><b>KmerCountingBloomFilter16</b> = <a class="el" href="classbtllib_1_1KmerCountingBloomFilter.html">KmerCountingBloomFilter</a><uint16_t></td></tr>
<tr class="separator:a37cec0aa234dbc5f9eb174bf3dd6f11a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af76b16b9df081a71bdc9403f7500586e" id="r_af76b16b9df081a71bdc9403f7500586e"><td class="memItemLeft" align="right" valign="top"><a id="af76b16b9df081a71bdc9403f7500586e" name="af76b16b9df081a71bdc9403f7500586e"></a>
using </td><td class="memItemRight" valign="bottom"><b>KmerCountingBloomFilter32</b> = <a class="el" href="classbtllib_1_1KmerCountingBloomFilter.html">KmerCountingBloomFilter</a><uint32_t></td></tr>
<tr class="separator:af76b16b9df081a71bdc9403f7500586e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae4df9d8793e2100b2d9d63c855010961" id="r_ae4df9d8793e2100b2d9d63c855010961"><td class="memItemLeft" align="right" valign="top"><a id="ae4df9d8793e2100b2d9d63c855010961" name="ae4df9d8793e2100b2d9d63c855010961"></a>
using </td><td class="memItemRight" valign="bottom"><b>PipeId</b> = unsigned long</td></tr>
<tr class="separator:ae4df9d8793e2100b2d9d63c855010961"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa32f1243aa1b1cf2f4b3b5d4984d8e77" id="r_aa32f1243aa1b1cf2f4b3b5d4984d8e77"><td class="memItemLeft" align="right" valign="top"><a id="aa32f1243aa1b1cf2f4b3b5d4984d8e77" name="aa32f1243aa1b1cf2f4b3b5d4984d8e77"></a>
using </td><td class="memItemRight" valign="bottom"><b>PipelineId</b> = unsigned long</td></tr>
<tr class="separator:aa32f1243aa1b1cf2f4b3b5d4984d8e77"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="func-members" name="func-members"></a>
Functions</h2></td></tr>
<tr class="memitem:aca76001bbc4e5627654cd44ba0ea925a" id="r_aca76001bbc4e5627654cd44ba0ea925a"><td class="memItemLeft" align="right" valign="top"><a id="aca76001bbc4e5627654cd44ba0ea925a" name="aca76001bbc4e5627654cd44ba0ea925a"></a>
std::vector< SpacedSeed > </td><td class="memItemRight" valign="bottom"><b>aa_parse_seeds</b> (const std::vector< std::string > &seeds)</td></tr>
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<tr class="memitem:ac954d7c54d302d9f285beb797dbe84a5" id="r_ac954d7c54d302d9f285beb797dbe84a5"><td class="memItemLeft" align="right" valign="top">std::vector< std::vector< unsigned > > </td><td class="memItemRight" valign="bottom"><a class="el" href="#ac954d7c54d302d9f285beb797dbe84a5">parse_seeds</a> (const std::vector< std::string > &seed_strings)</td></tr>
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<tr class="memitem:a0c9cb0705283e0519330f79629cdc738" id="r_a0c9cb0705283e0519330f79629cdc738"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="#a0c9cb0705283e0519330f79629cdc738">reverse_complement</a> (std::string &seq)</td></tr>
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<tr class="memitem:abfd77a3465be4993f797a31a3b2a285b" id="r_abfd77a3465be4993f797a31a3b2a285b"><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="#abfd77a3465be4993f797a31a3b2a285b">get_reverse_complement</a> (const std::string &seq)</td></tr>
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<tr class="memitem:a716b22a3ebaccac72777988b3725bd5b" id="r_a716b22a3ebaccac72777988b3725bd5b"><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="#a716b22a3ebaccac72777988b3725bd5b">get_time</a> ()</td></tr>
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<tr class="memitem:aa0d6ecae33b5e60b5c285f5358a9ad6a" id="r_aa0d6ecae33b5e60b5c285f5358a9ad6a"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="#aa0d6ecae33b5e60b5c285f5358a9ad6a">log_info</a> (const std::string &msg)</td></tr>
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<tr class="memitem:a60a36f4583a7eb03001f8bdb7b395507" id="r_a60a36f4583a7eb03001f8bdb7b395507"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="#a60a36f4583a7eb03001f8bdb7b395507">check_warning</a> (bool condition, const std::string &msg)</td></tr>
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<tr class="memitem:a540bce0213b7718e519ddc4466361bf7" id="r_a540bce0213b7718e519ddc4466361bf7"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="#a540bce0213b7718e519ddc4466361bf7">check_error</a> (bool condition, const std::string &msg)</td></tr>
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std::string </td><td class="memItemRight" valign="bottom"><b>get_strerror</b> ()</td></tr>
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<tr class="memitem:a90573e7060c9c97d74316adf8faa75b0" id="r_a90573e7060c9c97d74316adf8faa75b0"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="#a90573e7060c9c97d74316adf8faa75b0">check_stream</a> (const std::ios &stream, const std::string &name)</td></tr>
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<tr class="memitem:aacf70cd44ded264af4f30ce3a4a4726a" id="r_aacf70cd44ded264af4f30ce3a4a4726a"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="#aacf70cd44ded264af4f30ce3a4a4726a">check_file_accessibility</a> (const std::string &filepath)</td></tr>
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<tr class="memitem:a6e1f7d38461cd2a81d5b070ae8a146fa" id="r_a6e1f7d38461cd2a81d5b070ae8a146fa"><td class="memItemLeft" align="right" valign="top">std::vector< std::string > </td><td class="memItemRight" valign="bottom"><a class="el" href="#a6e1f7d38461cd2a81d5b070ae8a146fa">split</a> (const std::string &s, const std::string &delim)</td></tr>
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<tr class="memitem:a3136b2f8753378b2712fb2c815c98a92" id="r_a3136b2f8753378b2712fb2c815c98a92"><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="#a3136b2f8753378b2712fb2c815c98a92">join</a> (const std::vector< std::string > &s, const std::string &delim)</td></tr>
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<tr class="memitem:ad74639e10aa8a303fc78973078e870dd" id="r_ad74639e10aa8a303fc78973078e870dd"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="#ad74639e10aa8a303fc78973078e870dd">ltrim</a> (std::string &s)</td></tr>
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void </td><td class="memItemRight" valign="bottom"><b>ltrim</b> (btllib::CString &s)</td></tr>
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<tr class="memitem:a8733bdc6b1d9fdbc9991a1150fb64401" id="r_a8733bdc6b1d9fdbc9991a1150fb64401"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="#a8733bdc6b1d9fdbc9991a1150fb64401">rtrim</a> (std::string &s)</td></tr>
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void </td><td class="memItemRight" valign="bottom"><b>rtrim</b> (btllib::CString &s)</td></tr>
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<tr class="memitem:a4d7c3b03ff4fe7ed419c723f3ddcfbd5" id="r_a4d7c3b03ff4fe7ed419c723f3ddcfbd5"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="#a4d7c3b03ff4fe7ed419c723f3ddcfbd5">trim</a> (std::string &s)</td></tr>
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void </td><td class="memItemRight" valign="bottom"><b>trim</b> (btllib::CString &s)</td></tr>
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<tr class="memitem:acc6df2bfa872c7b1e830cf314d20e306" id="r_acc6df2bfa872c7b1e830cf314d20e306"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="#acc6df2bfa872c7b1e830cf314d20e306">startswith</a> (std::string s, std::string prefix)</td></tr>
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<tr class="memitem:a0d3f4421a7f9ba97324ad2791a96e2b5" id="r_a0d3f4421a7f9ba97324ad2791a96e2b5"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="#a0d3f4421a7f9ba97324ad2791a96e2b5">endswith</a> (std::string s, std::string suffix)</td></tr>
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<tr class="memitem:a68b2069643d786fbf1036dc642ac788c" id="r_a68b2069643d786fbf1036dc642ac788c"><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="#a68b2069643d786fbf1036dc642ac788c">get_basename</a> (const std::string &path)</td></tr>
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<tr class="memitem:a5e2272b09bf4f9c60554a66eb4b664d2" id="r_a5e2272b09bf4f9c60554a66eb4b664d2"><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="#a5e2272b09bf4f9c60554a66eb4b664d2">get_dirname</a> (const std::string &path)</td></tr>
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<tr class="memitem:affa73b1930c10683bf0531af7473d4be" id="r_affa73b1930c10683bf0531af7473d4be"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="#affa73b1930c10683bf0531af7473d4be">sum_phred</a> (const std::string &qual, size_t start_pos=0, size_t len=0)</td></tr>
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<tr class="memitem:a5136f7df8791303fb0d812a82c87789a" id="r_a5136f7df8791303fb0d812a82c87789a"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="#a5136f7df8791303fb0d812a82c87789a">calc_phred_avg</a> (const std::string &qual, size_t start_pos=0, size_t len=0)</td></tr>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="var-members" name="var-members"></a>
Variables</h2></td></tr>
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const char </td><td class="memItemRight" valign="bottom"><b>COMPLEMENTS</b> [256]</td></tr>
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const char </td><td class="memItemRight" valign="bottom"><b>AMINO_ACIDS</b> [256]</td></tr>
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const char </td><td class="memItemRight" valign="bottom"><b>CAPITALS</b> [256]</td></tr>
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constexpr const char * </td><td class="memItemRight" valign="bottom"><b>PRINT_COLOR_INFO</b> = "\33[32m"</td></tr>
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constexpr const char * </td><td class="memItemRight" valign="bottom"><b>PRINT_COLOR_WARNING</b> = "\33[33m"</td></tr>
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constexpr const char * </td><td class="memItemRight" valign="bottom"><b>PRINT_COLOR_ERROR</b> = "\33[31m"</td></tr>
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constexpr const char * </td><td class="memItemRight" valign="bottom"><b>PRINT_COLOR_END</b> = "\33[0m"</td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Functions for sequence manipulation.</p>
<p>Functions for logging and error checking.</p>
<p>Random utility functions. </p>
</div><h2 class="groupheader">Function Documentation</h2>
<a id="a5136f7df8791303fb0d812a82c87789a" name="a5136f7df8791303fb0d812a82c87789a"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a5136f7df8791303fb0d812a82c87789a">◆ </a></span>calc_phred_avg()</h2>
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<td class="memname">double btllib::calc_phred_avg </td>
<td>(</td>
<td class="paramtype">const std::string &</td> <td class="paramname"><span class="paramname"><em>qual</em></span>, </td>
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<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">size_t</td> <td class="paramname"><span class="paramname"><em>start_pos</em></span><span class="paramdefsep"> = </span><span class="paramdefval">0</span>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">size_t</td> <td class="paramname"><span class="paramname"><em>len</em></span><span class="paramdefsep"> = </span><span class="paramdefval">0</span> )</td>
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</div><div class="memdoc">
<p>Calculate the average phred score of a string, depending on the start position and length.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">qual</td><td>The quality string to calculate the average from. </td></tr>
<tr><td class="paramname">start_pos</td><td>The start position of the substring. Defaults to 0. </td></tr>
<tr><td class="paramname">len</td><td>The length of the substring. Defaults to 0. If 0, the whole string is used.</td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>The average phred score of the substring. </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a540bce0213b7718e519ddc4466361bf7">◆ </a></span>check_error()</h2>
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<td class="memname">void btllib::check_error </td>
<td>(</td>
<td class="paramtype">bool</td> <td class="paramname"><span class="paramname"><em>condition</em></span>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">const std::string &</td> <td class="paramname"><span class="paramname"><em>msg</em></span> )</td>
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<p>Conditionally log error level events. The program exits if the condition is true.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">condition</td><td>If this is true, the message is printed and the program exits. </td></tr>
<tr><td class="paramname">msg</td><td>Message to print. </td></tr>
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</dd>
</dl>
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<h2 class="memtitle"><span class="permalink"><a href="#aacf70cd44ded264af4f30ce3a4a4726a">◆ </a></span>check_file_accessibility()</h2>
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<td class="memname">void btllib::check_file_accessibility </td>
<td>(</td>
<td class="paramtype">const std::string &</td> <td class="paramname"><span class="paramname"><em>filepath</em></span></td><td>)</td>
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<p>Check whether the file at the given path is accessible (exists, permissions are good, etc.).</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">filepath</td><td>Path to the file to check. </td></tr>
</table>
</dd>
</dl>
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<h2 class="memtitle"><span class="permalink"><a href="#ae35010b35086565ec1bdf8f454c99d3a">◆ </a></span>check_info()</h2>
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<td class="memname">void btllib::check_info </td>
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<td class="paramtype">bool</td> <td class="paramname"><span class="paramname"><em>condition</em></span>, </td>
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<p>Conditionally log info level events.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">condition</td><td>If this is true, the message is printed. </td></tr>
<tr><td class="paramname">msg</td><td>Message to print. </td></tr>
</table>
</dd>
</dl>
</div>
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<h2 class="memtitle"><span class="permalink"><a href="#a90573e7060c9c97d74316adf8faa75b0">◆ </a></span>check_stream()</h2>
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<td class="memname">void btllib::check_stream </td>
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<td class="paramtype">const std::ios &</td> <td class="paramname"><span class="paramname"><em>stream</em></span>, </td>
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<p>Check whether the stream is good. Program prints an error message and exits if not.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">stream</td><td>Stream to check goodness of. </td></tr>
<tr><td class="paramname">name</td><td>Name of the stream, e.g. filepath or stdin </td></tr>
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</dd>
</dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a60a36f4583a7eb03001f8bdb7b395507">◆ </a></span>check_warning()</h2>
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<td class="memname">void btllib::check_warning </td>
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<td class="paramtype">bool</td> <td class="paramname"><span class="paramname"><em>condition</em></span>, </td>
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<p>Conditionally log warning level events.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">condition</td><td>If this is true, the message is printed. </td></tr>
<tr><td class="paramname">msg</td><td>Message to print. </td></tr>
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</dd>
</dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a0d3f4421a7f9ba97324ad2791a96e2b5">◆ </a></span>endswith()</h2>
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<td class="memname">bool btllib::endswith </td>
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<td class="paramtype">std::string</td> <td class="paramname"><span class="paramname"><em>s</em></span>, </td>
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<td class="paramtype">std::string</td> <td class="paramname"><span class="paramname"><em>suffix</em></span> )</td>
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<p>Check whether the given string ends with a suffix.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">s</td><td>String to check. </td></tr>
<tr><td class="paramname">suffix</td><td>Suffix to check for. </td></tr>
</table>
</dd>
</dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a68b2069643d786fbf1036dc642ac788c">◆ </a></span>get_basename()</h2>
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<td class="memname">std::string btllib::get_basename </td>
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<td class="paramtype">const std::string &</td> <td class="paramname"><span class="paramname"><em>path</em></span></td><td>)</td>
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<p>Equivalent to the GNU implementation of basename, but returns a string copy of the result.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">path</td><td>The path to get basename from.</td></tr>
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</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>The basename of the path. </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a5e2272b09bf4f9c60554a66eb4b664d2">◆ </a></span>get_dirname()</h2>
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<td class="memname">std::string btllib::get_dirname </td>
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<td class="paramtype">const std::string &</td> <td class="paramname"><span class="paramname"><em>path</em></span></td><td>)</td>
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<p>Equivalent to the GNU implementation of dirname, but returns a string copy of the result.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">path</td><td>The path to get dirname from.</td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>The dirname of the path. </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#abfd77a3465be4993f797a31a3b2a285b">◆ </a></span>get_reverse_complement()</h2>
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<td class="memname">std::string btllib::get_reverse_complement </td>
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<td class="paramtype">const std::string &</td> <td class="paramname"><span class="paramname"><em>seq</em></span></td><td>)</td>
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<p>Obtain a reverse complement of the provided sequence. The argument sequence is left untouched.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">seq</td><td>Sequence to reverse complement.</td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>Reverse complemented sequence. </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a716b22a3ebaccac72777988b3725bd5b">◆ </a></span>get_time()</h2>
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<td class="memname">std::string btllib::get_time </td>
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<p>Return current time as a string. </p>
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<h2 class="memtitle"><span class="permalink"><a href="#a3136b2f8753378b2712fb2c815c98a92">◆ </a></span>join()</h2>
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<td class="memname">std::string btllib::join </td>
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<td class="paramtype">const std::vector< std::string > &</td> <td class="paramname"><span class="paramname"><em>s</em></span>, </td>
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<td class="paramtype">const std::string &</td> <td class="paramname"><span class="paramname"><em>delim</em></span> )</td>
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<p>Join a vector of strings into a single string with a delimiter.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">s</td><td>Vector of strings to join. </td></tr>
<tr><td class="paramname">delim</td><td>Delimiter to join the strings with.</td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>String with all the components joined. </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#aae48e6ebdbbde9836cd2c20347b85606">◆ </a></span>log_error()</h2>
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<td class="memname">void btllib::log_error </td>
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<td class="paramtype">const std::string &</td> <td class="paramname"><span class="paramname"><em>msg</em></span></td><td>)</td>
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<p>Log error level events.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">msg</td><td>Message to print. </td></tr>
</table>
</dd>
</dl>
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<h2 class="memtitle"><span class="permalink"><a href="#aa0d6ecae33b5e60b5c285f5358a9ad6a">◆ </a></span>log_info()</h2>
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<td class="memname">void btllib::log_info </td>
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<td class="paramtype">const std::string &</td> <td class="paramname"><span class="paramname"><em>msg</em></span></td><td>)</td>
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<p>Log info level events.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">msg</td><td>Message to print. </td></tr>
</table>
</dd>
</dl>
</div>
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<h2 class="memtitle"><span class="permalink"><a href="#a3d4af2317963b43668700a59fb8c67a6">◆ </a></span>log_warning()</h2>
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<td class="memname">void btllib::log_warning </td>
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<td class="paramtype">const std::string &</td> <td class="paramname"><span class="paramname"><em>msg</em></span></td><td>)</td>
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<p>Log warning level events.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">msg</td><td>Message to print. </td></tr>
</table>
</dd>
</dl>
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<h2 class="memtitle"><span class="permalink"><a href="#ad74639e10aa8a303fc78973078e870dd">◆ </a></span>ltrim()</h2>
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<td class="memname">void btllib::ltrim </td>
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<td class="paramtype">std::string &</td> <td class="paramname"><span class="paramname"><em>s</em></span></td><td>)</td>
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<p>Trim whitespace on the left side of the given string.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">s</td><td>String to trim, edited in-place. </td></tr>
</table>
</dd>
</dl>
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<h2 class="memtitle"><span class="permalink"><a href="#ac954d7c54d302d9f285beb797dbe84a5">◆ </a></span>parse_seeds()</h2>
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<td class="memname">std::vector< std::vector< unsigned > > btllib::parse_seeds </td>
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<td class="paramtype">const std::vector< std::string > &</td> <td class="paramname"><span class="paramname"><em>seed_strings</em></span></td><td>)</td>
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<span class="mlabels"><span class="mlabel">inline</span></span> </td>
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<p>Parse each spaced seed pattern into lists of don't care positions. Legacy function used in btllib Bloom filters. </p>
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<h2 class="memtitle"><span class="permalink"><a href="#a0c9cb0705283e0519330f79629cdc738">◆ </a></span>reverse_complement()</h2>
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<td class="memname">void btllib::reverse_complement </td>
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<td class="paramtype">std::string &</td> <td class="paramname"><span class="paramname"><em>seq</em></span></td><td>)</td>
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<p>Reverse complement a sequence in-place.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">seq</td><td>Sequence to reverse complement. </td></tr>
</table>
</dd>
</dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a8733bdc6b1d9fdbc9991a1150fb64401">◆ </a></span>rtrim()</h2>
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<td class="memname">void btllib::rtrim </td>
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<td class="paramtype">std::string &</td> <td class="paramname"><span class="paramname"><em>s</em></span></td><td>)</td>
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<p>Trim whitespace on the right side of the given string.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">s</td><td>String to trim, edited in-place. </td></tr>
</table>
</dd>
</dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a6e1f7d38461cd2a81d5b070ae8a146fa">◆ </a></span>split()</h2>
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<td class="memname">std::vector< std::string > btllib::split </td>
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<td class="paramtype">const std::string &</td> <td class="paramname"><span class="paramname"><em>s</em></span>, </td>
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<td class="paramtype">const std::string &</td> <td class="paramname"><span class="paramname"><em>delim</em></span> )</td>
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<p>Split a string into component substrings with a delimiter.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">s</td><td>String to split. </td></tr>
<tr><td class="paramname">delim</td><td>Delimiter to split with.</td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>Vector of substrings delimited by <code>delim</code>, excluding delimiters themselves. </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#acc6df2bfa872c7b1e830cf314d20e306">◆ </a></span>startswith()</h2>
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<td class="memname">bool btllib::startswith </td>
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<td class="paramtype">std::string</td> <td class="paramname"><span class="paramname"><em>s</em></span>, </td>
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<td class="paramtype">std::string</td> <td class="paramname"><span class="paramname"><em>prefix</em></span> )</td>
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<p>Check whether the given string starts with a prefix.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">s</td><td>String to check. </td></tr>
<tr><td class="paramname">prefix</td><td>Prefix to check for. </td></tr>
</table>
</dd>
</dl>
</div>
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<h2 class="memtitle"><span class="permalink"><a href="#affa73b1930c10683bf0531af7473d4be">◆ </a></span>sum_phred()</h2>
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<td class="memname">double btllib::sum_phred </td>
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<td class="paramtype">const std::string &</td> <td class="paramname"><span class="paramname"><em>qual</em></span>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">size_t</td> <td class="paramname"><span class="paramname"><em>start_pos</em></span><span class="paramdefsep"> = </span><span class="paramdefval">0</span>, </td>
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<td class="paramtype">size_t</td> <td class="paramname"><span class="paramname"><em>len</em></span><span class="paramdefsep"> = </span><span class="paramdefval">0</span> )</td>
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<p>Calculate the sum of the phred scores of a string.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">qual</td><td>The quality string to calculate the sum from. </td></tr>
<tr><td class="paramname">start_pos</td><td>The start position of the substring. Defaults to 0. </td></tr>
<tr><td class="paramname">len</td><td>The length of the substring. Defaults to 0. If 0, the whole string is used.</td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>The sum of the phred scores of the substring. </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a4d7c3b03ff4fe7ed419c723f3ddcfbd5">◆ </a></span>trim()</h2>
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<td class="memname">void btllib::trim </td>
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<td class="paramtype">std::string &</td> <td class="paramname"><span class="paramname"><em>s</em></span></td><td>)</td>
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<p>Trim whitespace on the left and right side of the given string.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">s</td><td>String to trim, edited in-place. </td></tr>
</table>
</dd>
</dl>
</div>
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