Update API docs for 3.0.1

jtnystrom · Feb 13, 2023 · f93da32 · f93da32
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diff --git a/docs/com/jnpersson/discount/bucket/BucketStats$.html b/docs/com/jnpersson/discount/bucket/BucketStats$.html
@@ -144,16 +144,16 @@ <h1>Packages</h1>
                         <a href="CountReducer.html" title="A reducer that handles k-mer count values stored in the longsForK(k) + 1 tag position.">CountReducer</a>
                       </li><li class="current-entities indented4">
                         <span class="separator"></span>
-                        <a class="class" href="CountersSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule"></a>
-                        <a href="CountersSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule">CountersSubtractReducer</a>
+                        <a class="class" href="CountersSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule."></a>
+                        <a href="CountersSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule.">CountersSubtractReducer</a>
                       </li><li class="current-entities indented4">
                         <span class="separator"></span>
                         <a class="class" href="KmerBucket.html" title="A bucket that maintains some number of super-mers and associated tags (e.g."></a>
                         <a href="KmerBucket.html" title="A bucket that maintains some number of super-mers and associated tags (e.g.">KmerBucket</a>
                       </li><li class="current-entities indented4">
                         <span class="separator"></span>
-                        <a class="class" href="KmerSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule"></a>
-                        <a href="KmerSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule">KmerSubtractReducer</a>
+                        <a class="class" href="KmerSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule."></a>
+                        <a href="KmerSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule.">KmerSubtractReducer</a>
                       </li><li class="current-entities indented4">
                         <span class="separator"></span>
                         <a class="class" href="LeftReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.Left reduction rule"></a>

diff --git a/docs/com/jnpersson/discount/bucket/BucketStats.html b/docs/com/jnpersson/discount/bucket/BucketStats.html
@@ -144,16 +144,16 @@ <h1>Packages</h1>
                         <a href="CountReducer.html" title="A reducer that handles k-mer count values stored in the longsForK(k) + 1 tag position.">CountReducer</a>
                       </li><li class="current-entities indented4">
                         <span class="separator"></span>
-                        <a class="class" href="CountersSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule"></a>
-                        <a href="CountersSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule">CountersSubtractReducer</a>
+                        <a class="class" href="CountersSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule."></a>
+                        <a href="CountersSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule.">CountersSubtractReducer</a>
                       </li><li class="current-entities indented4">
                         <span class="separator"></span>
                         <a class="class" href="KmerBucket.html" title="A bucket that maintains some number of super-mers and associated tags (e.g."></a>
                         <a href="KmerBucket.html" title="A bucket that maintains some number of super-mers and associated tags (e.g.">KmerBucket</a>
                       </li><li class="current-entities indented4">
                         <span class="separator"></span>
-                        <a class="class" href="KmerSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule"></a>
-                        <a href="KmerSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule">KmerSubtractReducer</a>
+                        <a class="class" href="KmerSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule."></a>
+                        <a href="KmerSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule.">KmerSubtractReducer</a>
                       </li><li class="current-entities indented4">
                         <span class="separator"></span>
                         <a class="class" href="LeftReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.Left reduction rule"></a>

diff --git a/docs/com/jnpersson/discount/bucket/CountReducer.html b/docs/com/jnpersson/discount/bucket/CountReducer.html
@@ -144,16 +144,16 @@ <h1>Packages</h1>
                         <a href="" title="A reducer that handles k-mer count values stored in the longsForK(k) + 1 tag position.">CountReducer</a>
                       </li><li class="current-entities indented4">
                         <span class="separator"></span>
-                        <a class="class" href="CountersSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule"></a>
-                        <a href="CountersSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule">CountersSubtractReducer</a>
+                        <a class="class" href="CountersSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule."></a>
+                        <a href="CountersSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule.">CountersSubtractReducer</a>
                       </li><li class="current-entities indented4">
                         <span class="separator"></span>
                         <a class="class" href="KmerBucket.html" title="A bucket that maintains some number of super-mers and associated tags (e.g."></a>
                         <a href="KmerBucket.html" title="A bucket that maintains some number of super-mers and associated tags (e.g.">KmerBucket</a>
                       </li><li class="current-entities indented4">
                         <span class="separator"></span>
-                        <a class="class" href="KmerSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule"></a>
-                        <a href="KmerSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule">KmerSubtractReducer</a>
+                        <a class="class" href="KmerSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule."></a>
+                        <a href="KmerSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule.">KmerSubtractReducer</a>
                       </li><li class="current-entities indented4">
                         <span class="separator"></span>
                         <a class="class" href="LeftReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.Left reduction rule"></a>

diff --git a/docs/com/jnpersson/discount/bucket/CountersSubtractReducer.html b/docs/com/jnpersson/discount/bucket/CountersSubtractReducer.html
@@ -144,16 +144,16 @@ <h1>Packages</h1>
                         <a href="CountReducer.html" title="A reducer that handles k-mer count values stored in the longsForK(k) + 1 tag position.">CountReducer</a>
                       </li><li class="current-entities indented4">
                         <span class="separator"></span>
-                        <a class="class" href="" title="Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule"></a>
-                        <a href="" title="Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule">CountersSubtractReducer</a>
+                        <a class="class" href="" title="Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule."></a>
+                        <a href="" title="Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule.">CountersSubtractReducer</a>
                       </li><li class="current-entities indented4">
                         <span class="separator"></span>
                         <a class="class" href="KmerBucket.html" title="A bucket that maintains some number of super-mers and associated tags (e.g."></a>
                         <a href="KmerBucket.html" title="A bucket that maintains some number of super-mers and associated tags (e.g.">KmerBucket</a>
                       </li><li class="current-entities indented4">
                         <span class="separator"></span>
-                        <a class="class" href="KmerSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule"></a>
-                        <a href="KmerSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule">KmerSubtractReducer</a>
+                        <a class="class" href="KmerSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule."></a>
+                        <a href="KmerSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule.">KmerSubtractReducer</a>
                       </li><li class="current-entities indented4">
                         <span class="separator"></span>
                         <a class="class" href="LeftReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.Left reduction rule"></a>
@@ -210,7 +210,9 @@ <h4 id="signature" class="signature">
       </h4>
 
 
-          <div id="comment" class="fullcommenttop"><div class="comment cmt"><p>Implements the <a href="../spark/package$$Rule$$CountersSubtract$.html" class="extype" name="com.jnpersson.discount.spark.Rule.CountersSubtract">com.jnpersson.discount.spark.Rule.CountersSubtract</a> reduction rule</p></div><div class="toggleContainer block">
+          <div id="comment" class="fullcommenttop"><div class="comment cmt"><p>Implements the <a href="../spark/package$$Rule$$CountersSubtract$.html" class="extype" name="com.jnpersson.discount.spark.Rule.CountersSubtract">com.jnpersson.discount.spark.Rule.CountersSubtract</a> reduction rule.
+For each k-mer we calculate count_1 - count_2 and set the result to this value.
+Only positive counts are preserved in the output.</p></div><div class="toggleContainer block">
           <span class="toggle">
             Linear Supertypes
           </span>

diff --git a/docs/com/jnpersson/discount/bucket/KmerBucket.html b/docs/com/jnpersson/discount/bucket/KmerBucket.html
@@ -144,16 +144,16 @@ <h1>Packages</h1>
                         <a href="CountReducer.html" title="A reducer that handles k-mer count values stored in the longsForK(k) + 1 tag position.">CountReducer</a>
                       </li><li class="current-entities indented4">
                         <span class="separator"></span>
-                        <a class="class" href="CountersSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule"></a>
-                        <a href="CountersSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule">CountersSubtractReducer</a>
+                        <a class="class" href="CountersSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule."></a>
+                        <a href="CountersSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule.">CountersSubtractReducer</a>
                       </li><li class="current-entities indented4">
                         <span class="separator"></span>
                         <a class="class" href="" title="A bucket that maintains some number of super-mers and associated tags (e.g."></a>
                         <a href="" title="A bucket that maintains some number of super-mers and associated tags (e.g.">KmerBucket</a>
                       </li><li class="current-entities indented4">
                         <span class="separator"></span>
-                        <a class="class" href="KmerSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule"></a>
-                        <a href="KmerSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule">KmerSubtractReducer</a>
+                        <a class="class" href="KmerSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule."></a>
+                        <a href="KmerSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule.">KmerSubtractReducer</a>
                       </li><li class="current-entities indented4">
                         <span class="separator"></span>
                         <a class="class" href="LeftReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.Left reduction rule"></a>

diff --git a/docs/com/jnpersson/discount/bucket/KmerSubtractReducer.html b/docs/com/jnpersson/discount/bucket/KmerSubtractReducer.html
@@ -144,16 +144,16 @@ <h1>Packages</h1>
                         <a href="CountReducer.html" title="A reducer that handles k-mer count values stored in the longsForK(k) + 1 tag position.">CountReducer</a>
                       </li><li class="current-entities indented4">
                         <span class="separator"></span>
-                        <a class="class" href="CountersSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule"></a>
-                        <a href="CountersSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule">CountersSubtractReducer</a>
+                        <a class="class" href="CountersSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule."></a>
+                        <a href="CountersSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule.">CountersSubtractReducer</a>
                       </li><li class="current-entities indented4">
                         <span class="separator"></span>
                         <a class="class" href="KmerBucket.html" title="A bucket that maintains some number of super-mers and associated tags (e.g."></a>
                         <a href="KmerBucket.html" title="A bucket that maintains some number of super-mers and associated tags (e.g.">KmerBucket</a>
                       </li><li class="current-entities indented4">
                         <span class="separator"></span>
-                        <a class="class" href="" title="Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule"></a>
-                        <a href="" title="Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule">KmerSubtractReducer</a>
+                        <a class="class" href="" title="Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule."></a>
+                        <a href="" title="Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule.">KmerSubtractReducer</a>
                       </li><li class="current-entities indented4">
                         <span class="separator"></span>
                         <a class="class" href="LeftReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.Left reduction rule"></a>
@@ -210,7 +210,8 @@ <h4 id="signature" class="signature">
       </h4>
 
 
-          <div id="comment" class="fullcommenttop"><div class="comment cmt"><p>Implements the <a href="../spark/package$$Rule$$KmersSubtract$.html" class="extype" name="com.jnpersson.discount.spark.Rule.KmersSubtract">com.jnpersson.discount.spark.Rule.KmersSubtract</a> reduction rule</p></div><div class="toggleContainer block">
+          <div id="comment" class="fullcommenttop"><div class="comment cmt"><p>Implements the <a href="../spark/package$$Rule$$KmersSubtract$.html" class="extype" name="com.jnpersson.discount.spark.Rule.KmersSubtract">com.jnpersson.discount.spark.Rule.KmersSubtract</a> reduction rule.
+k-mers are kept if they existed in bucket A, but not in bucket B.</p></div><div class="toggleContainer block">
           <span class="toggle">
             Linear Supertypes
           </span>

diff --git a/docs/com/jnpersson/discount/bucket/LeftReducer.html b/docs/com/jnpersson/discount/bucket/LeftReducer.html
@@ -144,16 +144,16 @@ <h1>Packages</h1>
                         <a href="CountReducer.html" title="A reducer that handles k-mer count values stored in the longsForK(k) + 1 tag position.">CountReducer</a>
                       </li><li class="current-entities indented4">
                         <span class="separator"></span>
-                        <a class="class" href="CountersSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule"></a>
-                        <a href="CountersSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule">CountersSubtractReducer</a>
+                        <a class="class" href="CountersSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule."></a>
+                        <a href="CountersSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule.">CountersSubtractReducer</a>
                       </li><li class="current-entities indented4">
                         <span class="separator"></span>
                         <a class="class" href="KmerBucket.html" title="A bucket that maintains some number of super-mers and associated tags (e.g."></a>
                         <a href="KmerBucket.html" title="A bucket that maintains some number of super-mers and associated tags (e.g.">KmerBucket</a>
                       </li><li class="current-entities indented4">
                         <span class="separator"></span>
-                        <a class="class" href="KmerSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule"></a>
-                        <a href="KmerSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule">KmerSubtractReducer</a>
+                        <a class="class" href="KmerSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule."></a>
+                        <a href="KmerSubtractReducer.html" title="Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule.">KmerSubtractReducer</a>
                       </li><li class="current-entities indented4">
                         <span class="separator"></span>
                         <a class="class" href="" title="Implements the com.jnpersson.discount.spark.Rule.Left reduction rule"></a>