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<h3>
Dylan Aïssi pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/plink2">Debian Med / plink2</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink2/-/commit/ffd32fc52a25740848aba72e81fc1f075b08b4b5">ffd32fc5</a></strong>
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<span>by Dylan Aïssi</span>
<i>at 2021-12-04T09:28:50+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.00~a3-211125+dfsg</pre>
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<h4>7 changed files:</h4>
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<li class="file-stats">
<a href="#38cc88fc0f6f1d13fc1f3ba9501e086f78fd5c7b">
Makefile.src
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<li class="file-stats">
<a href="#d6636c923c1bfe7af3f61b1f50be13e844c67b52">
Python/pgenlib.pyx
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<li class="file-stats">
<a href="#b43b93cac30179c003057d2e68a314c13d2a399b">
Python/setup.py
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<li class="file-stats">
<a href="#f00a96fdb9f82e44f644dd8d17721446f31a8c50">
build_dynamic/Makefile
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<li class="file-stats">
<a href="#e828d66bb2fc597bda91bc643d9d9d5df9c3de2f">
plink2.cc
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<li class="file-stats">
<a href="#82c8c0946825d16815c68e845955a90079d70b6b">
plink2_glm.cc
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<li class="file-stats">
<a href="#de41b6d72d79193624852ea9511a56681eebfdb2">
plink2_help.cc
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<h4>Changes:</h4>
<li id="38cc88fc0f6f1d13fc1f3ba9501e086f78fd5c7b">
<a href="https://salsa.debian.org/med-team/plink2/-/commit/ffd32fc52a25740848aba72e81fc1f075b08b4b5#38cc88fc0f6f1d13fc1f3ba9501e086f78fd5c7b"><strong>Makefile.src</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,15 +9,25 @@ CSRC = include/SFMT.c libdeflate/lib/adler32.c libdeflate/lib/crc32.c libdeflate</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"><span class="nv" style="color: #008080;">ZCSRC</span> <span class="o" style="font-weight: 600;">=</span> zstd/lib/common/debug.c zstd/lib/common/entropy_common.c zstd/lib/common/zstd_common.c zstd/lib/common/error_private.c zstd/lib/common/xxhash.c zstd/lib/common/fse_decompress.c zstd/lib/common/pool.c zstd/lib/common/threading.c zstd/lib/compress/fse_compress.c zstd/lib/compress/hist.c zstd/lib/compress/huf_compress.c zstd/lib/compress/zstd_double_fast.c zstd/lib/compress/zstd_fast.c zstd/lib/compress/zstd_lazy.c zstd/lib/compress/zstd_ldm.c zstd/lib/compress/zstd_opt.c zstd/lib/compress/zstd_compress.c zstd/lib/compress/zstd_compress_literals.c zstd/lib/compress/zstd_compress_sequences.c zstd/lib/compress/zstd_compress_superblock.c zstd/lib/compress/zstdmt_compress.c zstd/lib/decompress/huf_decompress.c zstd/lib/decompress/zstd_decompress.c zstd/lib/decompress/zstd_ddict.c zstd/lib/decompress/zstd_decompress_block.c</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="make"><span class="nv" style="color: #008080;">CCSRC</span> <span class="o" style="font-weight: 600;">=</span> include/plink2_base.cc include/plink2_bits.cc include/pgenlib_misc.cc include/pgenlib_read.cc include/pgenlib_write.cc include/plink2_bgzf.cc include/plink2_stats.cc include/plink2_string.cc include/plink2_text.cc include/plink2_thread.cc include/plink2_zstfile.cc plink2.cc plink2_adjust.cc plink2_cmdline.cc plink2_common.cc plink2_compress_stream.cc plink2_data.cc plink2_decompress.cc plink2_export.cc plink2_fasta.cc plink2_filter.cc plink2_glm.cc plink2_help.cc plink2_import.cc plink2_ld.cc plink2_matrix.cc plink2_matrix_calc.cc plink2_merge.cc plink2_misc.cc plink2_psam.cc plink2_pvar.cc plink2_random.cc plink2_set.cc</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="make"><span class="nv" style="color: #008080;">PGENLIB_CCSRC</span> <span class="o" style="font-weight: 600;">=</span> include/plink2_base.cc include/plink2_bits.cc include/pgenlib_misc.cc include/pgenlib_read.cc include/pgenlib_write.cc</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="make"><span class="nv" style="color: #008080;">PLINK2LIB_CCSRC</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(PGENLIB_CCSRC)</span> include/plink2_bgzf.cc include/plink2_stats.cc include/plink2_string.cc include/plink2_text.cc include/plink2_thread.cc include/plink2_zstfile.cc</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="make"><span class="nv" style="color: #008080;">CCSRC</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(PLINK2LIB_CCSRC)</span> plink2.cc plink2_adjust.cc plink2_cmdline.cc plink2_common.cc plink2_compress_stream.cc plink2_data.cc plink2_decompress.cc plink2_export.cc plink2_fasta.cc plink2_filter.cc plink2_glm.cc plink2_help.cc plink2_import.cc plink2_ld.cc plink2_matrix.cc plink2_matrix_calc.cc plink2_merge.cc plink2_misc.cc plink2_psam.cc plink2_pvar.cc plink2_random.cc plink2_set.cc</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="make"><span class="nv" style="color: #008080;">OBJ_NO_ZSTD</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(CSRC:.c=.o)</span> <span class="nv" style="color: #008080;">$(CCSRC:.cc=.o)</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="make"><span class="nv" style="color: #008080;">OBJ</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(CSRC:.c=.o)</span> <span class="nv" style="color: #008080;">$(ZCSRC:.c=.o)</span> <span class="nv" style="color: #008080;">$(CCSRC:.cc=.o)</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="make"><span class="nv" style="color: #008080;">PGENLIB_OBJ</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(PGENLIB_CCSRC:.cc=.o)</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="make"><span class="nv" style="color: #008080;">PLINK2LIB_OBJ</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(CSRC:.c=.o)</span> <span class="nv" style="color: #008080;">$(ZCSRC:.c=.o)</span> <span class="nv" style="color: #008080;">$(PLINK2LIB_CCSRC:.cc=.o)</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="make"><span class="nv" style="color: #008080;">CSRC2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">foreach</span> fname,<span class="nv" style="color: #008080;">$(CSRC)</span>,../<span class="nv" style="color: #008080;">$(fname)</span><span class="nf" style="color: #900; font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="make"><span class="nv" style="color: #008080;">ZCSRC2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">foreach</span> fname,<span class="nv" style="color: #008080;">$(ZCSRC)</span>,../<span class="nv" style="color: #008080;">$(fname)</span><span class="nf" style="color: #900; font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="make"><span class="nv" style="color: #008080;">CCSRC2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">foreach</span> fname,<span class="nv" style="color: #008080;">$(CCSRC)</span>,../<span class="nv" style="color: #008080;">$(fname)</span><span class="nf" style="color: #900; font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="make"><span class="nv" style="color: #008080;">PGENLIB_CCSRC2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">foreach</span> fname,<span class="nv" style="color: #008080;">$(PGENLIB_CCSRC)</span>,../<span class="nv" style="color: #008080;">$(fname)</span><span class="nf" style="color: #900; font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="make"><span class="nv" style="color: #008080;">PLINK2LIB_CCSRC2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">foreach</span> fname,<span class="nv" style="color: #008080;">$(PLINK2LIB_CCSRC)</span>,../<span class="nv" style="color: #008080;">$(fname)</span><span class="nf" style="color: #900; font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="make"><span class="nv" style="color: #008080;">OBJ2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">notdir</span> <span class="nv" style="color: #008080;">$(OBJ)</span><span class="nf" style="color: #900; font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="make"><span class="nv" style="color: #008080;">PGENLIB_OBJ2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">notdir</span> <span class="nv" style="color: #008080;">$(PGENLIB_OBJ)</span><span class="nf" style="color: #900; font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="make"><span class="nv" style="color: #008080;">PLINK2LIB_OBJ2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">notdir</span> <span class="nv" style="color: #008080;">$(PLINK2LIB_OBJ)</span><span class="nf" style="color: #900; font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="make"><span class="nv" style="color: #008080;">OBJ3</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(CSRC2:.c=.o)</span> <span class="nv" style="color: #008080;">$(ZCSRC2:.c=.o)</span> <span class="nv" style="color: #008080;">$(CCSRC2:.cc=.o)</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="make"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,7 +38,7 @@ CXXINCLUDE2 = -I../simde</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="make"><span class="nv" style="color: #008080;">ZSTD_INCLUDE</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-Izstd</span>/lib <span class="nt" style="color: #000080;">-Izstd</span>/lib/common</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="make"><span class="nv" style="color: #008080;">ZSTD_INCLUDE2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-I</span>../zstd/lib <span class="nt" style="color: #000080;">-I</span>../zstd/lib/common</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="make"><span class="nv" style="color: #008080;">PGCSRC</span> <span class="o" style="font-weight: 600;">=</span> <span class="idiff left right">include/plink2_base.cc include/plink2_bits.cc include/pgenlib_misc.cc include/pgenlib_read.cc include/pgenlib_write.cc</span> pgen_compress.cc</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="make"><span class="nv" style="color: #008080;">PGCSRC</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;"><span class="idiff left right">$(PGENLIB_CCSRC)</span></span> pgen_compress.cc</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="make"><span class="nv" style="color: #008080;">PGCOBJ</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(PGCSRC:.cc=.o)</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="make"><span class="nv" style="color: #008080;">PGCSRC2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">foreach</span> fname,<span class="nv" style="color: #008080;">$(PGCSRC)</span>,../<span class="nv" style="color: #008080;">$(fname)</span><span class="nf" style="color: #900; font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="make"></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/commit/ffd32fc52a25740848aba72e81fc1f075b08b4b5#d6636c923c1bfe7af3f61b1f50be13e844c67b52"><strong>Python/pgenlib.pyx</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1130,12 +1130,12 @@ cdef class PgenReader:</td>
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<pre style="margin: 0;"> <span id="LC1130" class="line" lang="cython"> <span class="nf" style="color: #900; font-weight: 600;">CleanupPgfi</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_info_ptr</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">reterr</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1131" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_info_ptr</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">vrtypes</span><span class="p">:</span></span>
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1132
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1132
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<pre style="margin: 0;"> <span id="LC1132" class="line" lang="cython"> <span class="nf" style="color: #900; font-weight: 600;">aligned_free</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_info_ptr</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">vrtypes</span><span class="p">)</span></span>
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1133
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<td class="new_line diff-line-num old" data-linenumber="1133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1133" class="line" lang="cython"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_state_ptr</span><span class="p">:</span></span>
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1134
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<td class="new_line diff-line-num old" data-linenumber="1133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1134" class="line" lang="cython"> <span class="idiff left right"> </span><span class="nf" style="color: #900; font-weight: 600;">CleanupPgr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_state_ptr</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">reterr</span><span class="p">)</span></span>
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1135
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<td class="new_line diff-line-num old" data-linenumber="1133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1135" class="line" lang="cython"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">PgrGetFreadBuf</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_state_ptr</span><span class="p">):</span></span>
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1136
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<td class="new_line diff-line-num old" data-linenumber="1133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1136" class="line" lang="cython"> <span class="idiff left right"> </span><span class="nf" style="color: #900; font-weight: 600;">aligned_free</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">PgrGetFreadBuf</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_state_ptr</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1137
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<td class="new_line diff-line-num old" data-linenumber="1133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1137" class="line" lang="cython"> <span class="idiff left right"> </span><span class="nf" style="color: #900; font-weight: 600;">PyMem_Free</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_state_ptr</span><span class="p">)</span></span>
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1138
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<td class="new_line diff-line-num old" data-linenumber="1133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1138" class="line" lang="cython"> <span class="idiff left right"> </span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_state_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NULL</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1133
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<pre style="margin: 0;">+<span id="LC1133" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_state_ptr</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1134
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<pre style="margin: 0;">+<span id="LC1134" class="line" lang="cython"> <span class="nf" style="color: #900; font-weight: 600;">CleanupPgr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_state_ptr</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">reterr</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1135
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<pre style="margin: 0;">+<span id="LC1135" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">PgrGetFreadBuf</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_state_ptr</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1136
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<pre style="margin: 0;">+<span id="LC1136" class="line" lang="cython"> <span class="nf" style="color: #900; font-weight: 600;">aligned_free</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">PgrGetFreadBuf</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_state_ptr</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1137
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<pre style="margin: 0;">+<span id="LC1137" class="line" lang="cython"> <span class="nf" style="color: #900; font-weight: 600;">PyMem_Free</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_state_ptr</span><span class="p">)</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="1138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1138
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<pre style="margin: 0;">+<span id="LC1138" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_state_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NULL</span></span>
</pre>
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1139
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<td class="new_line diff-line-num" data-linenumber="1139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1139
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<pre style="margin: 0;"> <span id="LC1139" class="line" lang="cython"> <span class="nf" style="color: #900; font-weight: 600;">PyMem_Free</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_info_ptr</span><span class="p">)</span></span>
</pre>
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1140
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1140
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<pre style="margin: 0;"> <span id="LC1140" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_info_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NULL</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="1141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1141
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<td class="new_line diff-line-num" data-linenumber="1141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1141
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<pre style="margin: 0;"> <span id="LC1141" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kPglRetSuccess</span><span class="p">:</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1154,11 +1154,11 @@ cdef class PgenReader:</td>
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1154
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<td class="new_line diff-line-num" data-linenumber="1154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1154
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<pre style="margin: 0;"> <span id="LC1154" class="line" lang="cython"> <span class="nf" style="color: #900; font-weight: 600;">CleanupPgfi</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_info_ptr</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">reterr</span><span class="p">)</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="1155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1155
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1155
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<pre style="margin: 0;"> <span id="LC1155" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_info_ptr</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">vrtypes</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1156
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<td class="new_line diff-line-num" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1156
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<pre style="margin: 0;"> <span id="LC1156" class="line" lang="cython"> <span class="nf" style="color: #900; font-weight: 600;">aligned_free</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_info_ptr</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">vrtypes</span><span class="p">)</span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC1157" class="line" lang="cython"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_state_ptr</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC1158" class="line" lang="cython"> <span class="idiff left right"> </span><span class="nf" style="color: #900; font-weight: 600;">CleanupPgr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_state_ptr</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">reterr</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1159" class="line" lang="cython"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">PgrGetFreadBuf</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_state_ptr</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC1160" class="line" lang="cython"> <span class="idiff left right"> </span><span class="nf" style="color: #900; font-weight: 600;">aligned_free</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">PgrGetFreadBuf</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_state_ptr</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC1161" class="line" lang="cython"> <span class="idiff left right"> </span><span class="nf" style="color: #900; font-weight: 600;">PyMem_Free</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_state_ptr</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC1157" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_state_ptr</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC1158" class="line" lang="cython"> <span class="nf" style="color: #900; font-weight: 600;">CleanupPgr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_state_ptr</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">reterr</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC1159" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">PgrGetFreadBuf</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_state_ptr</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC1160" class="line" lang="cython"> <span class="nf" style="color: #900; font-weight: 600;">aligned_free</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">PgrGetFreadBuf</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_state_ptr</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC1161" class="line" lang="cython"> <span class="nf" style="color: #900; font-weight: 600;">PyMem_Free</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_state_ptr</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1162" class="line" lang="cython"> <span class="nf" style="color: #900; font-weight: 600;">PyMem_Free</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_info_ptr</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1163" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,6 +21,6 @@ ext_modules = [</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"> <span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="n" style="color: #333;">setup</span><span class="p">(</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Pgenlib'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'0.7<span class="idiff left right">5</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'0.7<span class="idiff left right">6</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">description</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Wrapper for pgenlib's basic reader and writer."</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">ext_modules</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cythonize</span><span class="p">(</span><span class="n" style="color: #333;">ext_modules</span><span class="p">))</span></span></pre>
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<a href="https://salsa.debian.org/med-team/plink2/-/commit/ffd32fc52a25740848aba72e81fc1f075b08b4b5#f00a96fdb9f82e44f644dd8d17721446f31a8c50"><strong>build_dynamic/Makefile</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -106,6 +106,8 @@ else</td>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="make"> <span class="nv" style="color: #008080;">LINKFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-lzstd</span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="make"><span class="nv" style="color: #008080;">LIBTOOL</span><span class="o" style="font-weight: 600;">=</span>ar</span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="make"><span class="nv" style="color: #008080;">STATIC</span><span class="o" style="font-weight: 600;">=</span>rcs</span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="make"><span class="nv" style="color: #008080;">UNAME</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> <span class="nb" style="color: #0086b3;">uname</span><span class="nf" style="color: #900; font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">($(UNAME), Darwin)</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="make"> <span class="k" style="font-weight: 600;">ifdef</span> <span class="nv" style="color: #008080;">FORCE_32BIT</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -118,6 +120,8 @@ ifeq ($(UNAME), Darwin)</td>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="make"> <span class="nv" style="color: #008080;">CFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-I</span>/usr/local/include</span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="make"> <span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-I</span>/usr/local/include <span class="nt" style="color: #000080;">-stdlib</span><span class="o" style="font-weight: 600;">=</span>libc++</span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="make"> <span class="nv" style="color: #008080;">LINKFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-L</span>/usr/local/lib</span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="make"> <span class="nv" style="color: #008080;">LIBTOOL</span><span class="o" style="font-weight: 600;">=</span>libtool</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="make"> <span class="nv" style="color: #008080;">STATIC</span><span class="o" style="font-weight: 600;">=</span><span class="nt" style="color: #000080;">-static</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="make"><span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="make"> <span class="k" style="font-weight: 600;">ifdef</span> <span class="nv" style="color: #008080;">DYNAMIC_MKL</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="make"> <span class="k" style="font-weight: 600;">ifdef</span> <span class="nv" style="color: #008080;">NO_LAPACK</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -159,8 +163,28 @@ plink2$(SFX): $(CSRC2) $(ZCSRC2) $(CCSRC2) ../plink2_cpu.cc</td>
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159
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="make"><span class="nl">pgen_compress$(SFX)</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(PGCSRC2)</span></span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CXX)</span> <span class="nv" style="color: #008080;">$(CXXFLAGS)</span> <span class="nv" style="color: #008080;">$(PGCSRC2)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span></span>
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="make"><span class="nl">pgenlib.a</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(PGENLIB_CCSRC2)</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CXX)</span> <span class="nv" style="color: #008080;">$(CXXFLAGS)</span> <span class="nv" style="color: #008080;">$(PGENLIB_CCSRC2)</span> <span class="nt" style="color: #000080;">-c</span></span>
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<td class="new_line diff-line-num new" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="make"> <span class="nv" style="color: #008080;">$(LIBTOOL)</span> <span class="nv" style="color: #008080;">$(STATIC)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$(PGENLIB_OBJ2)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="make"></span>
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<td class="new_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="make"><span class="nl">plink2lib.a</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(CSRC2) $(ZCSRC2) $(PLINK2LIB_CCSRC2)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CC)</span> <span class="nv" style="color: #008080;">$(CFLAGS)</span> <span class="nv" style="color: #008080;">$(CSRC2)</span> <span class="nt" style="color: #000080;">-c</span></span>
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<td class="new_line diff-line-num new" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CC)</span> <span class="nv" style="color: #008080;">$(ZCFLAGS)</span> <span class="nv" style="color: #008080;">$(ZCSRC2)</span> <span class="nt" style="color: #000080;">-c</span></span>
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<td class="new_line diff-line-num new" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CXX)</span> <span class="nv" style="color: #008080;">$(CXXFLAGS)</span> <span class="nv" style="color: #008080;">$(PLINK2LIB_CCSRC2)</span> <span class="nt" style="color: #000080;">-c</span></span>
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<td class="new_line diff-line-num new" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="make"> <span class="nv" style="color: #008080;">$(LIBTOOL)</span> <span class="nv" style="color: #008080;">$(STATIC)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$(PLINK2LIB_OBJ2)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="make"></span>
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<td class="new_line diff-line-num new" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="make"><span class="nl">static_pgenlib_test</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">pgenlib.a ../pgen_compress.cc</span></span>
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<td class="new_line diff-line-num new" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CXX)</span> <span class="nv" style="color: #008080;">$(CXXFLAGS)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> ../pgen_compress.cc <span class="nt" style="color: #000080;">-L</span><span class="nb" style="color: #0086b3;">.</span> pgenlib.a</span>
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<td class="new_line diff-line-num new" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="make"></span>
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<td class="new_line diff-line-num new" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="make"><span class="nl">static_plink2lib_test</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">plink2lib.a ../pgen_compress.cc</span></span>
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<td class="new_line diff-line-num new" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CXX)</span> <span class="nv" style="color: #008080;">$(CXXFLAGS)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> ../pgen_compress.cc <span class="nt" style="color: #000080;">-L</span><span class="nb" style="color: #0086b3;">.</span> plink2lib.a</span>
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<td class="new_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="make"></span>
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162
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<td class="new_line diff-line-num" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">clean</span></span>
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163
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<td class="new_line diff-line-num" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="make"><span class="nl">clean</span><span class="o" style="font-weight: 600;">:</span></span>
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164
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<td class="new_line diff-line-num" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> <span class="k" style="font-weight: 600;">*</span>.o</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
165
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<td class="new_line diff-line-num" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> plink2</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
166
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<td class="new_line diff-line-num" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> pgen_compress</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> pgenlib.a</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> plink2lib.a</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> static_pgenlib_test</span>
</pre>
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> static_plink2lib_test</span></pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -71,7 +71,7 @@ static const char ver_str[] = "PLINK v2.00a3"</td>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="">#ifdef USE_MKL</span>
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang=""> " Intel"</span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="">#endif</span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang=""> " (<span class="idiff left right">11 Oct</span> 2021)";</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang=""> " (<span class="idiff left right">25 Nov</span> 2021)";</span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="">static const char ver_str2[] =</span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang=""> // include leading space if day < 10, so character length stays the same</span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang=""> ""</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -728,7 +728,7 @@ uint32_t CheckForSeparatedCatCovar(const uintptr_t* pheno_cc, const uintptr_t* c</td>
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<pre style="margin: 0;"> <span id="LC728" class="line" lang=""> if (!case_and_ctrl_cat_ct) {</span>
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<pre style="margin: 0;"> <span id="LC729" class="line" lang=""> return 2;</span>
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<pre style="margin: 0;"> <span id="LC730" class="line" lang=""> }</span>
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<pre style="margin: 0;">-<span id="LC731" class="line" lang=""> if (case_and_ctrl_cat_ct == pheno_by_cat_ct<span class="idiff left right"> * 2</span>) {</span>
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<pre style="margin: 0;">+<span id="LC731" class="line" lang=""> if (case_and_ctrl_cat_ct <span class="idiff left right">* 2 </span>== pheno_by_cat_ct) {</span>
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<pre style="margin: 0;"> <span id="LC732" class="line" lang=""> // all categories contain both cases and controls.</span>
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<pre style="margin: 0;"> <span id="LC733" class="line" lang=""> return 0;</span>
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<pre style="margin: 0;"> <span id="LC734" class="line" lang=""> }</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1294,8 +1294,9 @@ PglErr DispHelp(const char* const* argvk, uint32_t param_ct) {</td>
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<pre style="margin: 0;"> <span id="LC1294" class="line" lang="cpp"><span class="s" style="color: #d14;">" chrX.)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1295
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<pre style="margin: 0;"> <span id="LC1295" class="line" lang="cpp"><span class="s" style="color: #d14;">" * The 'se' modifier causes the input coefficients to be treated as</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC1296" class="line" lang="cpp"><span class="s" style="color: #d14;">" independent standard errors; in this case, standard errors for the score</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1297
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<pre style="margin: 0;">-<span id="LC1297" class="line" lang="cpp"><span class="s" style="color: #d14;">" average/sum are reported. (Note that this will systematically</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC1298" class="line" lang="cpp"><span class="s" style="color: #d14;">" underestimate standard errors when scored variants are in LD.)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC1297" class="line" lang="cpp"><span class="s" style="color: #d14;">" average/sum are reported, under a Gaussian approximation. (Note that</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC1298" class="line" lang="cpp"><span class="s" style="color: #d14;">" this will systematically underestimate standard errors when scored</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC1299" class="line" lang="cpp"><span class="s" style="color: #d14;">" variants are in LD.)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC1300" class="line" lang="cpp"><span class="s" style="color: #d14;">" * By default, --score errors out if a variant ID in the input file appears</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC1301" class="line" lang="cpp"><span class="s" style="color: #d14;">" multiple times in the main dataset. Use the 'ignore-dup-ids' modifier to</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC1302" class="line" lang="cpp"><span class="s" style="color: #d14;">" skip them instead (a warning is still printed if such variants are</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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