<div dir="ltr"><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">This is the v1.4 release of khmer featuring the results of our March and April (PyCon) coding sprints and the 16 new contributors; the use of the new v0.8 release of screed (the library we use for pure Python reading of nucleotide sequence files); and the addition of <a href="https://github.com/luizirber" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@luizirber</a>&#39;s HyperLogLog counter for quick cardinality estimation.</p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Documentation is at <a href="https://khmer.readthedocs.org/en/v1.4/" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">https://khmer.readthedocs.org/en/v1.4/</a></p><h2 style="margin-top:1em;margin-bottom:16px;line-height:1.225;font-size:1.75em;padding-bottom:0.3em;border-bottom-width:1px;border-bottom-style:solid;border-bottom-color:rgb(238,238,238);color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif">New items of note:</h2><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Casava 1.8 read naming is now fully supported and in general the scripts no longer mangle read names. Side benefits: <code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">split-paired-reads.py</code> will no longer drop reads with &#39;bad&#39; names;<code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">count-median.py</code> can generate output in CSV format. <a href="https://github.com/ged-lab/khmer/pull/759" class="issue-link" title="&quot;broken&quot; paired-read support for a few scripts" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#759</a> <a href="https://github.com/ged-lab/khmer/pull/818" class="issue-link" title="Explore a fix for broken casava format handling in a number of scripts" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#818</a> <a href="https://github.com/ctb" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@ctb</a> <a href="https://github.com/ged-lab/khmer/issues/873" class="issue-link" title="split-paired-reads.py breaks" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#873</a> <a href="https://github.com/ahaerpfer" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@ahaerpfer</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Most scripts now support a &quot;broken&quot; interleaved paired-read format for FASTA/FASTQ nucleotide sequence files. <a href="http://khmer.readthedocs.org/en/v1.4/user/scripts.html#trim-low-abund-py" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent"><code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">trim-low-abund.py</code></a> has been promoted from the sandbox as well (with streaming support). <a href="https://github.com/ged-lab/khmer/pull/759" class="issue-link" title="&quot;broken&quot; paired-read support for a few scripts" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#759</a> <a href="https://github.com/ctb" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@ctb</a> <a href="https://github.com/ged-lab/khmer/pull/963" class="issue-link" title="Added STDOUT streaming support for scripts/trim-low-abund.py" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#963</a> <a href="https://github.com/sguermond" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@sguermond</a> <a href="https://github.com/ged-lab/khmer/pull/933" class="issue-link" title="Add (broken interleaved) paired-end support to sample-reads-randomly.py script. Closes #899." style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#933</a> <a href="https://github.com/standage" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@standage</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">The script to transform an interleaved paired-read nucleotide sequence file into two files now allows one to name the output files which can be useful in combination with named pipes for streaming processing <a href="https://github.com/ged-lab/khmer/pull/762" class="issue-link" title="update split-paired-reads to support -1 and -2 options" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#762</a> <a href="https://github.com/ctb" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@ctb</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Streaming everywhere: thanks to screed v0.8 we now support streaming of almost all inputs and outputs. <a href="https://github.com/ged-lab/khmer/pull/830" class="issue-link" title="Fix/787" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#830</a> <a href="https://github.com/aditi9783" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@aditi9783</a> <a href="https://github.com/ged-lab/khmer/pull/812" class="issue-link" title="ReadParser s/accuracy/quality/g" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#812</a> <a href="https://github.com/mr-c" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@mr-c</a> <a href="https://github.com/ged-lab/khmer/pull/917" class="issue-link" title="screed 0.8" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#917</a> <a href="https://github.com/bocajnotnef" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@bocajnotnef</a> <a href="https://github.com/ged-lab/khmer/pull/882" class="issue-link" title="Option for printing diginorm output to stdout. Closes #881." style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#882</a> <a href="https://github.com/standage" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@standage</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Need a quick way to count total number of unique k-mers in very low memory? the <code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">unique-kmers.py</code> script in the sandbox uses a HyperLogLog counter to quickly (and with little memory) provide an estimate with a controllable error rate. <a href="https://github.com/ged-lab/khmer/pull/257" class="issue-link" title="HyperLogLog Counter" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#257</a> <a href="https://github.com/ged-lab/khmer/pull/738" class="issue-link" title="HLL coverage improvements" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#738</a> <a href="https://github.com/ged-lab/khmer/pull/895" class="issue-link" title="Remove unused versions of MurmurHash3; fix #888" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#895</a> <a href="https://github.com/ged-lab/khmer/pull/902" class="issue-link" title="Use for loop instead of transform" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#902</a> <a href="https://github.com/luizirber" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@luizirber</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px"><code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">normalize-by-median.py</code> can now process both a paired interleaved sequence file and a file of unpaired reads in the same invocation thus removing the need to write the counting table to disk as required in the workaround. <a href="https://github.com/ged-lab/khmer/pull/957" class="issue-link" title="Fix Issuer #58: normalize-by-median: accept paired &amp; unpaired data at the same time" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#957</a> <a href="https://github.com/susinmotion" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@susinmotion</a></p><h2 style="margin-top:1em;margin-bottom:16px;line-height:1.225;font-size:1.75em;padding-bottom:0.3em;border-bottom-width:1px;border-bottom-style:solid;border-bottom-color:rgb(238,238,238);color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif">Notable bugs fixed/issues closed:</h2><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Paired-end reads from Casava 1.8 no longer require renaming for use in <code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">normalize-by-median.py</code> and <code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">abund-filter.py</code> when used in paired mode <a href="https://github.com/ged-lab/khmer/pull/818" class="issue-link" title="Explore a fix for broken casava format handling in a number of scripts" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#818</a> <a href="https://github.com/ctb" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@ctb</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Python version support clarified. We do not (yet) support Python 3.x <a href="https://github.com/ged-lab/khmer/pull/741" class="issue-link" title="clarify py version req" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#741</a> <a href="https://github.com/mr-c" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@mr-c</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">If a single output file mode is chosen for normalize-by-median.py we now default to overwriting the output. Appending the output is available by using the append redirection operator from the shell. <a href="https://github.com/ged-lab/khmer/pull/843" class="issue-link" title="Fix the append behavior in normalize-by-median.py (#745)" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#843</a> <a href="https://github.com/drtamermansour" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@drtamermansour</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Scripts that consume sequence data using C++ will now properly throw an error on truncated files.<a href="https://github.com/ged-lab/khmer/pull/897" class="issue-link" title="Throw exception on weird seqan parsing of truncated file" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#897</a> <a href="https://github.com/kdmurray91" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@kdmurray91</a> <br style>And while writing to disk we properly check for errors <a href="https://github.com/ged-lab/khmer/pull/856" class="issue-link" title="check for errors while writing to disk" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#856</a> <a href="https://github.com/ged-lab/khmer/pull/962" class="issue-link" title="remove memory leak" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#962</a> <a href="https://github.com/mr-c" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@mr-c</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px"><code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">abundance-dist-single.py</code> no longer fails with small files and many threads. <a href="https://github.com/ged-lab/khmer/pull/900" class="issue-link" title="add thread safety to CountingHash::abundance_distribtion" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#900</a> <a href="https://github.com/mr-c" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@mr-c</a></p><h2 style="margin-top:1em;margin-bottom:16px;line-height:1.225;font-size:1.75em;padding-bottom:0.3em;border-bottom-width:1px;border-bottom-style:solid;border-bottom-color:rgb(238,238,238);color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif">Additional fixes/features</h2><h3 style="margin-top:1em;margin-bottom:16px;line-height:1.43;font-size:1.5em;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif">Of interest to users:</h3><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Many documentation updates <a href="https://github.com/ged-lab/khmer/pull/753" class="issue-link" title="Add link to PR checklist in CONTRIBUTING.md" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#753</a> <a href="https://github.com/PamelaM" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@PamelaM</a>, <a href="https://github.com/ged-lab/khmer/pull/782" class="issue-link" title="Fixed docs #778, #779, #780" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#782</a> <a href="https://github.com/bocajnotnef" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@bocajnotnef</a>, <a href="https://github.com/ged-lab/khmer/pull/845" class="issue-link" title="Add citation information for hll algorithm" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#845</a> <a href="https://github.com/alameldin" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@alameldin</a>, <a href="https://github.com/ged-lab/khmer/pull/804" class="issue-link" title="Corrected spelling errors in doc/dev/coding-guidelines-and-review.txt" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#804</a><a href="https://github.com/ctb" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@ctb</a>, <a href="https://github.com/ged-lab/khmer/pull/870" class="issue-link" title="Fix/793" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#870</a> <a href="https://github.com/SchwarzEM" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@SchwarzEM</a>, <a href="https://github.com/ged-lab/khmer/pull/953" class="issue-link" title="small edit to release-notes; added repo to top of main docs page" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#953</a> <a href="https://github.com/ged-lab/khmer/pull/942" class="issue-link" title="started editing docs to add &quot;how to get help&quot;" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#942</a> <a href="https://github.com/safay" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@safay</a>, <a href="https://github.com/ged-lab/khmer/pull/929" class="issue-link" title="Update documentation for force and squash options" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#929</a>,<a href="https://github.com/davelin1" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@davelin1</a>, <a href="https://github.com/ged-lab/khmer/pull/687" class="issue-link" title="add a ReadTheDocs badge" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#687</a> <a href="https://github.com/ged-lab/khmer/pull/912" class="issue-link" title="doc/*.txt -&gt; *.rst" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#912</a> <a href="https://github.com/ged-lab/khmer/pull/926" class="issue-link" title="Add links to chat" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#926</a> <a href="https://github.com/mr-c" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@mr-c</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Installation instructions for Conda, Arch Linux, and Mac Ports have been added <a href="https://github.com/ged-lab/khmer/pull/723" class="issue-link" title="Added documentation for Arch Linux" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#723</a><a href="https://github.com/reedacartwright" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@reedacartwright</a> <a href="https://github.com/ged-lab/khmer/pull/952" class="issue-link" title="Fix/777" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#952</a> <a href="https://github.com/elmbeech" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@elmbeech</a> <a href="https://github.com/ged-lab/khmer/pull/930" class="issue-link" title="Update getting started info for Conda users." style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#930</a> <a href="https://github.com/ahaerpfer" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@ahaerpfer</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">The example script for the STAMPS database has been fixed to run correctly <a href="https://github.com/ged-lab/khmer/pull/781" class="issue-link" title="fix #780 - Update do.sh" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#781</a><a href="https://github.com/drtamermansour" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@drtamermansour</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px"><code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">split-paired-reads.py</code>: added <code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">-o</code> option to allow specification of an output directory <a href="https://github.com/ged-lab/khmer/pull/752" class="issue-link" title="Enable specification of output directory" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#752</a><a href="https://github.com/bede" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@bede</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Fixed a string formatting and a boundry error in <code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">sample-reads-randomly.py</code> <a href="https://github.com/ged-lab/khmer/pull/773" class="issue-link" title="fix a glitch about string formatting in sample-reads-randomly.py" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#773</a> <a href="https://github.com/qingpeng" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@qingpeng</a><a href="https://github.com/ged-lab/khmer/pull/995" class="issue-link" title="fixed boundary error in sample-reads-randomly" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#995</a> <a href="https://github.com/ctb" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@ctb</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">CSV output added to <code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">abundance-dist.py</code>, <code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">abundance-dist-single.py</code>, and <code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">count-overlap.py</code>, and <code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">readstats.py</code> <a href="https://github.com/ged-lab/khmer/pull/831" class="issue-link" title="Output CSV format in abundance-dist.py" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#831</a> <a href="https://github.com/ged-lab/khmer/pull/854" class="issue-link" title="CVS output to abundance-test-single.py" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#854</a> <a href="https://github.com/ged-lab/khmer/pull/855" class="issue-link" title="Add csv option to count overlap.py" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#855</a> <a href="https://github.com/drtamermansour" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@drtamermansour</a> <a href="https://github.com/ged-lab/khmer/pull/959" class="issue-link" title="Fix/840" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#959</a> <a href="https://github.com/anotherthomas" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@anotherthomas</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">TSV/JSON output of <code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">load-into-counting.py</code> enhanced with the total number of reads processed <a href="https://github.com/ged-lab/khmer/pull/996" class="issue-link" title="Add total number of reads to summary json/tsv" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#996</a> <a href="https://github.com/kdmurray91" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@kdmurray91</a> <br style>Output files are now also checked to be writable <em style>before</em> loading the input files <a href="https://github.com/ged-lab/khmer/pull/672" class="issue-link" title="Fix Issue 669: Check that output and info files in load-into-counting.py are writable before loading input" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#672</a> <a href="https://github.com/pgarland" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@pgarland</a><a href="https://github.com/bocajnotnef" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@bocajnotnef</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px"><code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">interleave-reads.py</code> now prints the output filename nicely <a href="https://github.com/ged-lab/khmer/pull/827" class="issue-link" title="Make interleave-reads.py print output name nicely" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#827</a> <a href="https://github.com/kdmurray91" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@kdmurray91</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Cleaned up error for input file not existing <a href="https://github.com/ged-lab/khmer/pull/772" class="issue-link" title="Start of issue 718, file not existing clean up" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#772</a> <a href="https://github.com/jessicamizzi" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@jessicamizzi</a> <a href="https://github.com/ged-lab/khmer/pull/851" class="issue-link" title="fix sandbox scripts for kfile changes" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#851</a> <a href="https://github.com/ctb" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@ctb</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Fixed error in <code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">find-knots.py</code> <a href="https://github.com/ged-lab/khmer/pull/860" class="issue-link" title="Fixed check_file_status error" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#860</a> <a href="https://github.com/TheOneHyer" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@TheOneHyer</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">The help text for <code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">load-into-counting.py</code> for the <code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">--no-bigcounts</code>/<code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">-b</code> flag has been clarified<a href="https://github.com/ged-lab/khmer/pull/857" class="issue-link" title="Make the help text of load-into-counting&#39;s &#39;-b&#39; flag more verbose" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#857</a> <a href="https://github.com/kdmurray91" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@kdmurray91</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px"><a href="https://github.com/lexnederbragt" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@lexnederbragt</a> confirmed an old bug has been fixed with his test for whitespace in sequence identifiers interacting with the <code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">extract-partitions.py</code> script <a href="https://github.com/ged-lab/khmer/pull/979" class="issue-link" title="Adding a test to extract_partitions: whitespace in fasta sequence header..." style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#979</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Now safe to copy-and-paste from the user documentation as the smart quotes have been turned off. <a href="https://github.com/ged-lab/khmer/pull/967" class="issue-link" title="Disable smart rendering in Sphinx config (#958)." style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#967</a> <a href="https://github.com/ahaerpfer" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@ahaerpfer</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">The script <code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">make-coverage.py</code> has been restored to the sandbox. <a href="https://github.com/ged-lab/khmer/pull/920" class="issue-link" title="Return the script &#39;make-coverage.py&#39; to sandbox " style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#920</a> <a href="https://github.com/SherineAwad" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@SherineAwad</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px"><code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">normalize-by-median.py</code> will warn if two of the input files have the same name <a href="https://github.com/ged-lab/khmer/pull/932" class="issue-link" title="@ normalize-by-median.py : multiple same named input files will now rais..." style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#932</a><a href="https://github.com/elmbeech" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@elmbeech</a></p><h3 style="margin-top:1em;margin-bottom:16px;line-height:1.43;font-size:1.5em;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif">Of interest to developers:</h3><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Switched away from using <code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">--user</code> install for developers <a href="https://github.com/ged-lab/khmer/pull/740" class="issue-link" title="no more --user installs" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#740</a> <a href="https://github.com/mr-c" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@mr-c</a> <a href="https://github.com/drtamermansour" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@drtamermansour</a> &amp;<a href="https://github.com/ged-lab/khmer/issues/883" class="issue-link" title="coverage from median k-mer count -&gt;  coverage on nucleotide level" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#883</a> <a href="https://github.com/standage" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@standage</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Developers can now see a summary of important Makefile targets via <code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">make help</code> <a href="https://github.com/ged-lab/khmer/pull/783" class="issue-link" title="Implemented rustic CLI for the makefile" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#783</a><a href="https://github.com/standage" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@standage</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">The unused <code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">khmer.load_pe</code> module has been removed <a href="https://github.com/ged-lab/khmer/pull/828" class="issue-link" title="Remove khmer.load_pe module" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#828</a> <a href="https://github.com/kdmurray91" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@kdmurray91</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Versioneer bug due to new screed release was squashed <a href="https://github.com/ged-lab/khmer/pull/835" class="issue-link" title="work around versioneer bug" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#835</a> <a href="https://github.com/mr-c" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@mr-c</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">A Python 2.6 and 2.7.2 specific bug was worked around <a href="https://github.com/ged-lab/khmer/pull/869" class="issue-link" title="Skip the get_raw_tables test if python doesn&#39;t  have memoryview" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#869</a> <a href="https://github.com/kdmurray91" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@kdmurray91</a> <a href="https://github.com/ctb" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@ctb</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">added functions hash_find_all_tags_list and hash_get_tags_and_positions to CountingHash objects <a href="https://github.com/ged-lab/khmer/pull/749" class="issue-link" title="Added mechanisms for retrieving tags by position within a sequence" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#749</a> <a href="https://github.com/ged-lab/khmer/pull/765" class="issue-link" title="post merge cleanup of #749" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#765</a> <a href="https://github.com/ctb" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@ctb</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">The <code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">make diff-cover</code> and ChangeLog formatting requirements have been added to checklist<a href="https://github.com/ged-lab/khmer/pull/766" class="issue-link" title="add diff-cover &amp; ChangeLog formatting requirements to checklist" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#766</a> <a href="https://github.com/mr-c" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@mr-c</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">A useful message is now presented if large tables fail to allocate enough memory <a href="https://github.com/ged-lab/khmer/pull/704" class="issue-link" title="recast std::bad_alloc as a Python exception" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#704</a> <a href="https://github.com/mr-c" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@mr-c</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">A checklist for developers adding new CPython types was added <a href="https://github.com/ged-lab/khmer/pull/727" class="issue-link" title="update ReadAligner to modern Python class + docs" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#727</a> <a href="https://github.com/mr-c" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@mr-c</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">The sandbox graduation checklist has been updated to include streaming support <a href="https://github.com/ged-lab/khmer/pull/951" class="issue-link" title="Added script I/O requirements" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#951</a><a href="https://github.com/sguermond" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@sguermond</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Specific policies for sandbox/ and scripts/ content, and a process for adding new command line scripts into scripts/ have been added to the developer documentation <a href="https://github.com/ged-lab/khmer/pull/799" class="issue-link" title="Policies for sandbox/ and scripts/ code, together with a process for moving code into scripts/" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#799</a> <a href="https://github.com/ctb" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@ctb</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Sandbox scripts update: corrected #! Python invocation <a href="https://github.com/ged-lab/khmer/pull/815" class="issue-link" title="Amend shebang line in sandbox scripts for python2" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#815</a> <a href="https://github.com/Echelon9" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@Echelon9</a>, executable bits, copyright headers, no underscores in filenames <a href="https://github.com/ged-lab/khmer/pull/823" class="issue-link" title="Setting executable bits on three files in sandbox Fix/798" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#823</a> <a href="https://github.com/ged-lab/khmer/pull/826" class="issue-link" title="add copyright header Fix/797" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#826</a> <a href="https://github.com/ged-lab/khmer/pull/850" class="issue-link" title="renaming the sandbox/ scripts to be lowercase" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#850</a> <a href="https://github.com/alameldin" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@alameldin</a> several scripts deleted, docs + requirements updated <a href="https://github.com/ged-lab/khmer/pull/852" class="issue-link" title="more sandbox cleanup" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#852</a> <a href="https://github.com/ctb" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@ctb</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Avoid running big-memory tests on OS X <a href="https://github.com/ged-lab/khmer/pull/819" class="issue-link" title="Avoiding running big-memory requests on OS X" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#819</a> <a href="https://github.com/ctb" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@ctb</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Unused callback code was removed <a href="https://github.com/ged-lab/khmer/pull/698" class="issue-link" title="remove unused callback code" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#698</a> <a href="https://github.com/mr-c" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@mr-c</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">The CPython code was updated to use the new checklist and follow additional best practices<a href="https://github.com/ged-lab/khmer/pull/785" class="issue-link" title="Some _khmermodule.cc refactoring" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#785</a> <a href="https://github.com/ged-lab/khmer/pull/842" class="issue-link" title="Fix coding style" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#842</a> <a href="https://github.com/luizirber" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@luizirber</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Added a read-only view of the raw counting tables <a href="https://github.com/ged-lab/khmer/pull/671" class="issue-link" title="Initial implementation of read-only buffer access to raw tables" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#671</a> <a href="https://github.com/camillescott" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@camillescott</a> <a href="https://github.com/ged-lab/khmer/pull/869" class="issue-link" title="Skip the get_raw_tables test if python doesn&#39;t  have memoryview" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#869</a> <a href="https://github.com/kdmurray91" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@kdmurray91</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Added a Python method for quickly getting the number of underlying tables in a counting or presence table <a href="https://github.com/ged-lab/khmer/pull/879" class="issue-link" title="Add CountingHash::n_tables() accessor" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#879</a> <a href="https://github.com/ged-lab/khmer/pull/880" class="issue-link" title="Add n_tables accessor to Hashbits" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#880</a> <a href="https://github.com/kdmurray91" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@kdmurray91</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">The C++ library can now be built separately for the brave and curious developer <a href="https://github.com/ged-lab/khmer/pull/788" class="issue-link" title="./lib Makefile rewrite, create libkhmer.{a,so} and install target" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#788</a><a href="https://github.com/kdmurray91" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@kdmurray91</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">The ReadParser object now keeps track of the number of reads processed <a href="https://github.com/ged-lab/khmer/pull/877" class="issue-link" title="Initial implementation of read counting in C++  read parser" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#877</a> <a href="https://github.com/kdmurray91" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@kdmurray91</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Documentation is now reproducible <a href="https://github.com/ged-lab/khmer/pull/886" class="issue-link" title="make doc gen repro" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#886</a> <a href="https://github.com/mr-c" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@mr-c</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Python future proofing: specify floor division <a href="https://github.com/ged-lab/khmer/pull/863" class="issue-link" title="future proofing: specify floor division; PEP8 update" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#863</a> <a href="https://github.com/mr-c" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@mr-c</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Miscellaneous spelling fixes; thanks codespell! <a href="https://github.com/ged-lab/khmer/pull/867" class="issue-link" title="spelling fixes" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#867</a> <a href="https://github.com/mr-c" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@mr-c</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Debian package list update <a href="https://github.com/ged-lab/khmer/pull/984" class="issue-link" title="add git dependency" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#984</a> <a href="https://github.com/mr-c" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@mr-c</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px"><code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">khmer.kfile.check_file_status()</code> has been renamed to <code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">check_input_files()</code> <a href="https://github.com/ged-lab/khmer/pull/941" class="issue-link" title="check_file_status-&gt;check_input_files" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#941</a><a href="https://github.com/proteasome" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@proteasome</a><br style><code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">filter-abund.py</code> now uses it to check the input counting table <a href="https://github.com/ged-lab/khmer/pull/931" class="issue-link" title="added check_file_status() for input_table" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#931</a> <a href="https://github.com/safay" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@safay</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px"><code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">normalize-by-median.py</code> was refactored to not pass the ArgParse object around <a href="https://github.com/ged-lab/khmer/pull/965" class="issue-link" title="Fixes issue #964 Scripts/normalize-by-median.py Don&#39;t pass ArgParseObject to functions" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#965</a><a href="https://github.com/susinmotion" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@susinmotion</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Developer communication has been clarified <a href="https://github.com/ged-lab/khmer/pull/969" class="issue-link" title="clarified dev communication in getting-started.rst" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#969</a> <a href="https://github.com/sguermond" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@sguermond</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Tests using the &#39;fail_okay=true&#39; parameter to <code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">runscript</code> have been updated to confirm the correct error occurred. 3 faulty tests were fixed and the docs were clarified <a href="https://github.com/ged-lab/khmer/pull/968" class="issue-link" title="Fix Issue #948 - tests with `fail_okay=True` use asserts to confirm the correct failure type" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#968</a> <a href="https://github.com/ged-lab/khmer/pull/971" class="issue-link" title="fixing docs to remind folks to make sure tests fail for the right reasons" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#971</a><a href="https://github.com/susinmotion" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@susinmotion</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">FASTA test added for <code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">extract-long-sequences.py</code> <a href="https://github.com/ged-lab/khmer/pull/901" class="issue-link" title="split test for extract_long_sequences into test for fa and for fq" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#901</a> <a href="https://github.com/jessicamizzi" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@jessicamizzi</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">&#39;added silly test for empty file warning&#39; <a href="https://github.com/ged-lab/khmer/pull/557" class="issue-link" title="added silly test for empty file warning" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#557</a> <a href="https://github.com/wltrimbl" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@wltrimbl</a> <a href="https://github.com/bocajnotnef" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@bocajnotnef</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">A couple tests were made more resilient and some extra error checking added in CPython land<a href="https://github.com/ged-lab/khmer/pull/889" class="issue-link" title="catch more exceptions &amp; make a couple tests more robust" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#889</a> <a href="https://github.com/mr-c" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@mr-c</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Copyright added to pull request checklist <a href="https://github.com/ged-lab/khmer/pull/940" class="issue-link" title="added Copyright queston to commit checklist" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#940</a> <a href="https://github.com/sguermond" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@sguermond</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px"><code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">khmer_exception</code>s are now based on <code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">std::string</code>s which plugs a memory leak <a href="https://github.com/ged-lab/khmer/pull/938" class="issue-link" title="fixed memory management of khmer_exception" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#938</a><a href="https://github.com/anotherthomas" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@anotherthomas</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Python docstrings were made PEP257 compliant <a href="https://github.com/ged-lab/khmer/pull/936" class="issue-link" title="Add pep257 targets to Makefile in preparation of docstrings cleanup." style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#936</a> <a href="https://github.com/ahaerpfer" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@ahaerpfer</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Some C++ comments were converted to be Doxygen compliant <a href="https://github.com/ged-lab/khmer/pull/950" class="issue-link" title="Added a few doxygen comments to hashbits.cc" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#950</a> <a href="https://github.com/josiahseaman" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@josiahseaman</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">The counting and presence table warning logic was refactored and centralized <a href="https://github.com/ged-lab/khmer/pull/944" class="issue-link" title="Fix issue #21:  Refactor Hash Size Warning Logic into Common Module" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#944</a><a href="https://github.com/susinmotion" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@susinmotion</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">The release checklist was updated to better run the post-install tests <a href="https://github.com/ged-lab/khmer/pull/911" class="issue-link" title="Properly test installed khmer module post install" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#911</a> <a href="https://github.com/mr-c" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@mr-c</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">The unused method <code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">find_all_tags_truncate_on_abundance</code> was removed from the CPython API <a href="https://github.com/ged-lab/khmer/pull/924" class="issue-link" title="removes find_all_tags_truncate_on_abundance from python api" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#924</a> <a href="https://github.com/anotherthomas" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@anotherthomas</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">OS X warnings quieted <a href="https://github.com/ged-lab/khmer/pull/887" class="issue-link" title="quiet OSX build" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#887</a> <a href="https://github.com/mr-c" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@mr-c</a></p><h2 style="margin-top:1em;margin-bottom:16px;line-height:1.225;font-size:1.75em;padding-bottom:0.3em;border-bottom-width:1px;border-bottom-style:solid;border-bottom-color:rgb(238,238,238);color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif">Known issues:</h2><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">All of these are pre-existing.</p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Some users have reported that normalize-by-median.py will utilize more memory than it was configured for. This is being investigated in <a href="https://github.com/ged-lab/khmer/issues/266" class="issue-link" title="exceeding defined RAM limits" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#266</a></p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Some scripts only output FASTA even if given a FASTQ file. This issue is being tracked in <a href="https://github.com/ged-lab/khmer/issues/46" class="issue-link" title="All scripts should output the sequence format they take in (FASTA/FASTA, FASTQ/FASTQ) by default" style="color:rgb(65,131,196);text-decoration:none;background-color:transparent">#46</a></p><h2 style="margin-top:1em;margin-bottom:16px;line-height:1.225;font-size:1.75em;padding-bottom:0.3em;border-bottom-width:1px;border-bottom-style:solid;border-bottom-color:rgb(238,238,238);color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif">Contributors</h2><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px"><a href="https://github.com/ctb" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@ctb</a>, <a href="https://github.com/kdmurray91" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@kdmurray91</a>, <a href="https://github.com/mr-c" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@mr-c</a>, <a href="https://github.com/drtamermansour" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@drtamermansour</a>, <a href="https://github.com/luizirber" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@luizirber</a>, <a href="https://github.com/standage" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@standage</a>, <a href="https://github.com/bocajnotnef" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@bocajnotnef</a>, *<a href="https://github.com/susinmotion" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@susinmotion</a>, <a href="https://github.com/jessicamizzi" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@jessicamizzi</a>, *<a href="https://github.com/elmbeech" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@elmbeech</a>, *<a href="https://github.com/anotherthomas" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@anotherthomas</a>, *<a href="https://github.com/sguermond" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@sguermond</a>, *<a href="https://github.com/ahaerpfer" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@ahaerpfer</a>, *<a href="https://github.com/alameldin" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@alameldin</a>, *<a href="https://github.com/TheOneHyer" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@TheOneHyer</a>, *<a href="https://github.com/aditi9783" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@aditi9783</a>, *<a href="https://github.com/proteasome" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@proteasome</a>, *<a href="https://github.com/bede" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@bede</a>, *<a href="https://github.com/davelin1" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@davelin1</a>, <a href="https://github.com/Echelon9" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@Echelon9</a>, <br style>*<a href="https://github.com/reedacartwright" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@reedacartwright</a>, <a href="https://github.com/qingpeng" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@qingpeng</a>, *<a href="https://github.com/SchwarzEM" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@SchwarzEM</a>, *<a href="https://github.com/scottsievert" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@scottsievert</a>, <a href="https://github.com/PamelaM" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@PamelaM</a>,<a href="https://github.com/SherineAwad" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@SherineAwad</a>, *<a href="https://github.com/josiahseaman" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@josiahseaman</a>, *<a href="https://github.com/lexnederbragt" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@lexnederbragt</a>,</p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">* Indicates new contributors</p><h2 style="margin-top:1em;margin-bottom:16px;line-height:1.225;font-size:1.75em;padding-bottom:0.3em;border-bottom-width:1px;border-bottom-style:solid;border-bottom-color:rgb(238,238,238);color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif">Issue reporters</h2><p style="margin-top:0px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px;margin-bottom:0px!important"><a href="https://github.com/moorepants" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@moorepants</a>, <a href="https://github.com/teshomem" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@teshomem</a>, <a href="https://github.com/macmanes" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@macmanes</a>, <a href="https://github.com/lexnederbragt" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@lexnederbragt</a>, <a href="https://github.com/r-gaia-cs" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@r-gaia-cs</a>, <a href="https://github.com/magentashades" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent">@magentashades</a></p></div>