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<h3>
Aaron M. Ucko pushed to branch master
at <a href="https://salsa.debian.org/med-team/ncbi-vdb">Debian Med / ncbi-vdb</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/ncbi-vdb/-/commit/fffde5db10e63c63ccbcd810892ecd1452b8d1f8">fffde5db</a></strong>
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<span>by Aaron M. Ucko</span>
<i>at 2021-01-18T16:57:55-05:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ncbi-vdb 2.10.9+dfsg-2: cherry-pick fix_2.10.9_refseq_race.patch.
Fix a new race in asynchronous RefSeq loading code, per upstream
(https://github.com/ncbi/ncbi-vdb) commits 06152a5, cf92dca, and b342af2.
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<h4>3 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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+
debian/patches/fix_2.10.9_refseq_race.patch
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/ncbi-vdb/-/commit/fffde5db10e63c63ccbcd810892ecd1452b8d1f8#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">ncbi-vdb (2.10.9+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * d/p/fix_2.10.9_refseq_race.patch: Fix a new race in asynchronous</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> RefSeq loading code, per upstream (https://github.com/ncbi/ncbi-vdb) </span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> commits 06152a5, cf92dca, and b342af2.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Aaron M. Ucko <ucko@debian.org> Mon, 18 Jan 2021 16:57:54 -0500</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">ncbi-vdb (2.10.9+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * New upstream version</span>
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<li id="a5bb25ef9416f467faf17d2b820b35fcd9e6af04">
<a href="https://salsa.debian.org/med-team/ncbi-vdb/-/commit/fffde5db10e63c63ccbcd810892ecd1452b8d1f8#a5bb25ef9416f467faf17d2b820b35fcd9e6af04"><strong>debian/patches/fix_2.10.9_refseq_race.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Kenneth Durbrow <durbrowk@ncbi.nlm.nih.gov></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Mon, 18 Jan 2021 14:50:24 -0500</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Fix a new race in asynchronous RefSeq loading code.</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> Merge upstream (https://github.com/ncbi/ncbi-vdb) commits 06152a5,</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> cf92dca, and b342af2.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">--- a/libs/axf/refseq.c</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/libs/axf/refseq.c</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -31,6 +31,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> #include <vdb/cursor.h></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> #include <kproc/lock.h></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> #include <kproc/thread.h></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <klib/refcount.h></span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> #include "refseq.h"</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> #include <stdlib.h></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -45,6 +46,7 @@</span> typedef RefSeq Object;</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> #include "util.h"</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> struct RefSeqAsyncLoadInfo {</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ KRefcount refcount;</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> KThread *th;</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> KLock *mutex; /**< mostly guards the cursor against concurrent use */</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> VCursor const *curs; /**< can be used by either thread after acquiring the mutex */</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="p">@@ -57,16 +59,38 @@</span> struct RefSeqAsyncLoadInfo {</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> unsigned volatile miss; /**< ... how effective the bg thread was */</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> };</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+static void RefSeqAsyncLoadInfo_Release(RefSeqAsyncLoadInfo *const self)</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+{</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ switch (KRefcountDrop(&self->refcount, "RefSeqAsyncLoadInfo")) {</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ case krefWhack:</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ break;</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ case krefOkay:</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return;</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ default:</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ assert(!"valid refcount");</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ abort();</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ VCursorRelease(self->curs);</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ KLockRelease(self->mutex);</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ KThreadRelease(self->th);</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ free(self);</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+}</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> static rc_t RefSeqAsyncLoadInfoFree(RefSeqAsyncLoadInfo *const self)</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> {</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> rc_t rc = 0;</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> if (self) {</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ /* Synchronize with background thread in preparation for clean up */</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ KRefcountAdd(&self->refcount, "RefSeqAsyncLoadInfo"); // keep alive; let die at line 89</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ LOGMSG(klogDebug, "Foreground thread ending background thread");</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> KLockAcquire(self->mutex);</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> self->count = 0;</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> KLockUnlock(self->mutex);</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> KThreadWait(self->th, &rc);</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ LOGERR(klogDebug, rc, "Background thread ended");</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ RefSeqAsyncLoadInfo_Release(self);</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> if (rc)</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- LOGERR(klogErr, rc, "async loader thread failed");</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ LOGERR(klogErr, rc, "asynchronous loader thread failed");</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> }</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> return rc;</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> }</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="p">@@ -361,37 +385,37 @@</span> static rc_t runLoadThread(Object *self)</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> else if (!done && rc == 0)</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> rc = RC(rcXF, rcFunction, rcReading, rcData, rcInvalid);</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> }</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (rc == 0 && i == count) {</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (n != 0) {</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- while (n < 4) {</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- accum <<= 2;</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ++n;</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self->bases[j++] = accum;</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (n != 0) {</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ while (n < 4) {</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ accum <<= 2;</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ++n;</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> }</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self->bases[j++] = accum;</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ free(buffer);</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ LOGMSG(klogDebug, "Done background loading of reference");</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (rc == 0 && i == count) {</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> KLockAcquire(async->mutex);</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> async->loaded = i + first; /* last row was loaded */</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> async->count = 0;</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> KLockUnlock(async->mutex);</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> }</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- LOGMSG(klogDebug, "Done background loading of reference");</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> </span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> assert((atomic_read(&self->rwl) & 1) == 0); /* there is only one writer */</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> atomic_inc(&self->rwl); /* tell readers we want to update the state */</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> while (atomic_read(&self->rwl) != 1)</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> ;</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ /* readers are all waiting in the loop at line 445 */</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> self->reader = rc == 0 ? readNormal : readZero;</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> self->async = NULL;</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- atomic_dec(&self->rwl); /* state is updated; readers can continue */</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ atomic_dec(&self->rwl); /* state is updated; readers continue to line 448 */</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> if (rc == 0 && i == count) {</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> double const pct = 100.0 * (async->hits - async->miss) / async->hits;</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> </span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> PLOGMSG(klogDebug, (klogDebug, "Done with background loading of reference; preload was $(pct)%", "pct=%5.1f", (float)pct));</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> }</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- KLockRelease(async->mutex);</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- free(buffer);</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- VCursorRelease(async->curs);</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- free(async);</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ RefSeqAsyncLoadInfo_Release(async);</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ LOGERR(klogDebug, rc, "Background thread exiting");</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> </span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> return rc;</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> }</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="p">@@ -510,6 +534,7 @@</span> static RefSeqAsyncLoadInfo *RefSeqAsyncL</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> result->max_seq_len = readU32(&car[2], rr->first, curs, prc);</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> assert(result->max_seq_len % 4 == 0);</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> if (*prc == 0) {</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ KRefcountInit(&result->refcount, 1, "RefSeqAsyncLoadInfo", "init", "");</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> result->curs = curs;</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> VCursorAddRef(curs);</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> result->rr = *rr;</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/libs/axf/restore-read.c</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/libs/axf/restore-read.c</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="p">@@ -325,6 +325,7 @@</span> static void RestoreReadSharedFree(Restor</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> KRWLockRelease(self->rwl);</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> KRefcountWhack(&self->refcount, "RestoreReadShared");</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> free(self);</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ LOGMSG(klogDebug, "Released shared global RestoreRead data object");</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> }</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> </span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> static void RestoreReadSharedRelease(RestoreReadShared *const self)</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="p">@@ -361,6 +362,31 @@</span> static RestoreReadShared *getRestoreRead</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> return g_shared.ptr;</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> }</span>
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<td class="diff-line-num new new_line" data-linenumber="137" 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">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="138" 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">
138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+unsigned RestoreReadShared_getState(unsigned *refSeqs, unsigned *wgs, unsigned *errors, unsigned *activeRefSeqs)</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+{</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (g_shared.ptr) {</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rc_t rc = 0;</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ RestoreReadShared *const ptr = getRestoreReadShared(&rc);</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ RestoreReadSharedReader(ptr);</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ *refSeqs = ptr->refSeqs.entries;</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ *wgs = ptr->wgs.entries;</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ *errors = ptr->errors.entries;</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ *activeRefSeqs = 0;</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ {</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ unsigned i;</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (i = 0; i < *refSeqs; ++i) {</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (ptr->refSeqs.entry[i].object->async != NULL)</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ++*activeRefSeqs;</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ RestoreReadSharedReaderDone(ptr);</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ RestoreReadSharedRelease(ptr);</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return 1;</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else return 0;</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+}</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"> struct RestoreRead {</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"> VDBManager const *mgr;</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> RestoreReadShared *shared;</span></pre>
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<a href="https://salsa.debian.org/med-team/ncbi-vdb/-/commit/fffde5db10e63c63ccbcd810892ecd1452b8d1f8#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -14,3 +14,4 @@ i386-uint64_msbit.patch</td>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">fix_path_mbedtls.patch</span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">redefine_CALL_MBEDTLS.patch</span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"># fix_parallel_build.patch</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">fix_2.10.9_refseq_race.patch</span></pre>
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