Add option to set buffer/block size for orderedqueue/seqreader/indexlr

docs/annotated.html

@@ -70,23 +70,24 @@
 <tr id="row_0_" class="even"><td class="entry"><span style="width:0px;display:inline-block;">&#160;</span><span id="arr_0_" class="arrow" onclick="toggleFolder('0_')">&#9660;</span><span class="icona"><span class="icon">N</span></span><b>btllib</b></td><td class="desc"></td></tr>
 <tr id="row_0_0_"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classbtllib_1_1BloomFilter.html" target="_self">BloomFilter</a></td><td class="desc"></td></tr>
 <tr id="row_0_1_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classbtllib_1_1CountingBloomFilter.html" target="_self">CountingBloomFilter</a></td><td class="desc"></td></tr>
-<tr id="row_0_2_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span id="arr_0_2_" class="arrow" onclick="toggleFolder('0_2_')">&#9660;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classbtllib_1_1Indexlr.html" target="_self">Indexlr</a></td><td class="desc"></td></tr>
-<tr id="row_0_2_0_" class="even"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structbtllib_1_1Indexlr_1_1Flag.html" target="_self">Flag</a></td><td class="desc"></td></tr>
-<tr id="row_0_2_1_"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structbtllib_1_1Indexlr_1_1Minimizer.html" target="_self">Minimizer</a></td><td class="desc"></td></tr>
-<tr id="row_0_2_2_" class="even"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structbtllib_1_1Indexlr_1_1Read.html" target="_self">Read</a></td><td class="desc"></td></tr>
-<tr id="row_0_2_3_"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structbtllib_1_1Indexlr_1_1Record.html" target="_self">Record</a></td><td class="desc"></td></tr>
-<tr id="row_0_3_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classbtllib_1_1KmerBloomFilter.html" target="_self">KmerBloomFilter</a></td><td class="desc"></td></tr>
-<tr id="row_0_4_"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classbtllib_1_1KmerCountingBloomFilter.html" target="_self">KmerCountingBloomFilter</a></td><td class="desc"></td></tr>
-<tr id="row_0_5_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classbtllib_1_1NtHash.html" target="_self">NtHash</a></td><td class="desc"></td></tr>
-<tr id="row_0_6_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span id="arr_0_6_" class="arrow" onclick="toggleFolder('0_6_')">&#9660;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classbtllib_1_1OrderQueue.html" target="_self">OrderQueue</a></td><td class="desc"></td></tr>
-<tr id="row_0_6_0_" class="even"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structbtllib_1_1OrderQueue_1_1Block.html" target="_self">Block</a></td><td class="desc"></td></tr>
-<tr id="row_0_6_1_"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structbtllib_1_1OrderQueue_1_1Slot.html" target="_self">Slot</a></td><td class="desc"></td></tr>
-<tr id="row_0_7_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classbtllib_1_1SeedBloomFilter.html" target="_self">SeedBloomFilter</a></td><td class="desc"></td></tr>
-<tr id="row_0_8_"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classbtllib_1_1SeedNtHash.html" target="_self">SeedNtHash</a></td><td class="desc"></td></tr>
-<tr id="row_0_9_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span id="arr_0_9_" class="arrow" onclick="toggleFolder('0_9_')">&#9660;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classbtllib_1_1SeqReader.html" target="_self">SeqReader</a></td><td class="desc"></td></tr>
-<tr id="row_0_9_0_"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structbtllib_1_1SeqReader_1_1Flag.html" target="_self">Flag</a></td><td class="desc"></td></tr>
-<tr id="row_0_9_1_" class="even"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structbtllib_1_1SeqReader_1_1Record.html" target="_self">Record</a></td><td class="desc"></td></tr>
-<tr id="row_0_10_"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classbtllib_1_1SeqWriter.html" target="_self">SeqWriter</a></td><td class="desc"></td></tr>
+<tr id="row_0_2_"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structbtllib_1_1CString.html" target="_self">CString</a></td><td class="desc"></td></tr>
+<tr id="row_0_3_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span id="arr_0_3_" class="arrow" onclick="toggleFolder('0_3_')">&#9660;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classbtllib_1_1Indexlr.html" target="_self">Indexlr</a></td><td class="desc"></td></tr>
+<tr id="row_0_3_0_"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structbtllib_1_1Indexlr_1_1Flag.html" target="_self">Flag</a></td><td class="desc"></td></tr>
+<tr id="row_0_3_1_" class="even"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structbtllib_1_1Indexlr_1_1Minimizer.html" target="_self">Minimizer</a></td><td class="desc"></td></tr>
+<tr id="row_0_3_2_"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structbtllib_1_1Indexlr_1_1Read.html" target="_self">Read</a></td><td class="desc"></td></tr>
+<tr id="row_0_3_3_" class="even"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structbtllib_1_1Indexlr_1_1Record.html" target="_self">Record</a></td><td class="desc"></td></tr>
+<tr id="row_0_4_"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classbtllib_1_1KmerBloomFilter.html" target="_self">KmerBloomFilter</a></td><td class="desc"></td></tr>
+<tr id="row_0_5_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classbtllib_1_1KmerCountingBloomFilter.html" target="_self">KmerCountingBloomFilter</a></td><td class="desc"></td></tr>
+<tr id="row_0_6_"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classbtllib_1_1NtHash.html" target="_self">NtHash</a></td><td class="desc"></td></tr>
+<tr id="row_0_7_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span id="arr_0_7_" class="arrow" onclick="toggleFolder('0_7_')">&#9660;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classbtllib_1_1OrderQueue.html" target="_self">OrderQueue</a></td><td class="desc"></td></tr>
+<tr id="row_0_7_0_"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structbtllib_1_1OrderQueue_1_1Block.html" target="_self">Block</a></td><td class="desc"></td></tr>
+<tr id="row_0_7_1_" class="even"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structbtllib_1_1OrderQueue_1_1Slot.html" target="_self">Slot</a></td><td class="desc"></td></tr>
+<tr id="row_0_8_"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classbtllib_1_1SeedBloomFilter.html" target="_self">SeedBloomFilter</a></td><td class="desc"></td></tr>
+<tr id="row_0_9_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classbtllib_1_1SeedNtHash.html" target="_self">SeedNtHash</a></td><td class="desc"></td></tr>
+<tr id="row_0_10_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span id="arr_0_10_" class="arrow" onclick="toggleFolder('0_10_')">&#9660;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classbtllib_1_1SeqReader.html" target="_self">SeqReader</a></td><td class="desc"></td></tr>
+<tr id="row_0_10_0_" class="even"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structbtllib_1_1SeqReader_1_1Flag.html" target="_self">Flag</a></td><td class="desc"></td></tr>
+<tr id="row_0_10_1_"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structbtllib_1_1SeqReader_1_1Record.html" target="_self">Record</a></td><td class="desc"></td></tr>
+<tr id="row_0_11_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classbtllib_1_1SeqWriter.html" target="_self">SeqWriter</a></td><td class="desc"></td></tr>
 </table>
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 </div><!-- contents -->

docs/classbtllib_1_1Indexlr-members.html

@@ -77,10 +77,16 @@
   <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>get_minimizers</b>() (defined in <a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
   <tr bgcolor="#f0f0f0"><td class="entry"><b>HashedKmer</b> typedef (defined in <a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a></td><td class="entry"></td></tr>
   <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>Indexlr</b>(std::string seqfile, size_t k, size_t w, unsigned flags=0, unsigned threads=5, bool verbose=false, const btllib::BloomFilter &amp;bf1=Indexlr::dummy_bf(), const btllib::BloomFilter &amp;bf2=Indexlr::dummy_bf()) (defined in <a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
-  <tr bgcolor="#f0f0f0"><td class="entry"><b>MAX_SIMULTANEOUS_INDEXLRS</b> (defined in <a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a></td><td class="entry"><span class="mlabel">static</span></td></tr>
-  <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>output_bx</b>() const (defined in <a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
-  <tr bgcolor="#f0f0f0"><td class="entry"><b>output_id</b>() const (defined in <a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
-  <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>output_seq</b>() const (defined in <a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr bgcolor="#f0f0f0"><td class="entry"><b>long_mode</b>() const (defined in <a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>LONG_MODE_BLOCK_SIZE</b> (defined in <a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a></td><td class="entry"><span class="mlabel">static</span></td></tr>
+  <tr bgcolor="#f0f0f0"><td class="entry"><b>LONG_MODE_BUFFER_SIZE</b> (defined in <a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a></td><td class="entry"><span class="mlabel">static</span></td></tr>
+  <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>MAX_SIMULTANEOUS_INDEXLRS</b> (defined in <a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a></td><td class="entry"><span class="mlabel">static</span></td></tr>
+  <tr bgcolor="#f0f0f0"><td class="entry"><b>output_bx</b>() const (defined in <a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>output_id</b>() const (defined in <a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr bgcolor="#f0f0f0"><td class="entry"><b>output_seq</b>() const (defined in <a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>short_mode</b>() const (defined in <a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr bgcolor="#f0f0f0"><td class="entry"><b>SHORT_MODE_BLOCK_SIZE</b> (defined in <a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a></td><td class="entry"><span class="mlabel">static</span></td></tr>
+  <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>SHORT_MODE_BUFFER_SIZE</b> (defined in <a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a></td><td class="entry"><span class="mlabel">static</span></td></tr>
   <tr bgcolor="#f0f0f0"><td class="entry"><b>~Indexlr</b>() (defined in <a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1Indexlr.html">btllib::Indexlr</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
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