Merge branch 'ar/build-docs-update-changelog-0.1.11' into 'master'

Updates to changelog and online docs for 0.1.11 release

See merge request machine-learning/modkit!72

CHANGELOG.md

@@ -4,6 +4,15 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v0.1.11]
+### Fixes
+- [extract] Correctly handles duplex modBAMs when using `--include-bed`
+- Refactors handling of CRAM when sampling records. Fixes #35. Suggests to use BAM.
+### Adds
+- [extract] Output contains `ref_mod_strand` and `modified_primary_base`
+- [pileup] New option `--max-depth` allows increasing depth beyond default in hts-lib and sets the default to 8,000 in case it changes in hts-lib.
+
+
 ## [v0.1.11-rc1]
 ### Fixes
 - [extract] Correctly handles duplex modBAMs when using `--include-bed`

docs/intro_extract.html

@@ -166,15 +166,17 @@ <h2 id="description-of-output-table"><a class="header" href="#description-of-out
 <tr><td>4</td><td>chrom</td><td>name of aligned contig, or '.' if unmapped</td><td>str</td></tr>
 <tr><td>5</td><td>mod_strand</td><td>strand of the molecule the base modification is on</td><td>str</td></tr>
 <tr><td>6</td><td>ref_strand</td><td>strand of the reference the read is aligned to, or '.' if unmapped</td><td>str</td></tr>
-<tr><td>7</td><td>fw_soft_clipped_start</td><td>number of bases soft clipped from the start of the forward-oriented read</td><td>int</td></tr>
-<tr><td>8</td><td>fw_soft_clipped_end</td><td>number of bases soft clipped from the end of the forward-oriented read</td><td>int</td></tr>
-<tr><td>9</td><td>read_length</td><td>total length of the read</td><td>int</td></tr>
-<tr><td>10</td><td>mod_qual</td><td>probability of the base modification in the next column</td><td>int</td></tr>
-<tr><td>11</td><td>mod_code</td><td>base modification code from the MM tag</td><td>str</td></tr>
-<tr><td>12</td><td>base_qual</td><td>basecall quality score (phred)</td><td>int</td></tr>
-<tr><td>13</td><td>ref_kmer</td><td>reference 5-mer sequence context (center base is aligned base), '.' if unmapped</td><td>str</td></tr>
-<tr><td>14</td><td>query_kmer</td><td>read 5-mer sequence context (center base is aligned base)</td><td>str</td></tr>
-<tr><td>15</td><td>canonical_base</td><td>canonical base from the query sequence, from the MM tag</td><td>str</td></tr>
+<tr><td>7</td><td>ref_mod_strand</td><td>strand of the reference with the base modification, or '.' if unmapped</td><td>str</td></tr>
+<tr><td>8</td><td>fw_soft_clipped_start</td><td>number of bases soft clipped from the start of the forward-oriented read</td><td>int</td></tr>
+<tr><td>9</td><td>fw_soft_clipped_end</td><td>number of bases soft clipped from the end of the forward-oriented read</td><td>int</td></tr>
+<tr><td>10</td><td>read_length</td><td>total length of the read</td><td>int</td></tr>
+<tr><td>11</td><td>mod_qual</td><td>probability of the base modification in the next column</td><td>int</td></tr>
+<tr><td>12</td><td>mod_code</td><td>base modification code from the MM tag</td><td>str</td></tr>
+<tr><td>13</td><td>base_qual</td><td>basecall quality score (phred)</td><td>int</td></tr>
+<tr><td>14</td><td>ref_kmer</td><td>reference 5-mer sequence context (center base is aligned base), '.' if unmapped</td><td>str</td></tr>
+<tr><td>15</td><td>query_kmer</td><td>read 5-mer sequence context (center base is aligned base)</td><td>str</td></tr>
+<tr><td>16</td><td>canonical_base</td><td>canonical base from the query sequence, from the MM tag</td><td>str</td></tr>
+<tr><td>16</td><td>modified_primary_base</td><td>primary sequence base with the modification</td><td>str</td></tr>
 </tbody></table>
 </div>
 <h2 id="example-usages"><a class="header" href="#example-usages">Example usages:</a></h2>

docs/print.html

@@ -432,15 +432,17 @@ <h2 id="description-of-output-table"><a class="header" href="#description-of-out
 <tr><td>4</td><td>chrom</td><td>name of aligned contig, or '.' if unmapped</td><td>str</td></tr>
 <tr><td>5</td><td>mod_strand</td><td>strand of the molecule the base modification is on</td><td>str</td></tr>
 <tr><td>6</td><td>ref_strand</td><td>strand of the reference the read is aligned to, or '.' if unmapped</td><td>str</td></tr>
-<tr><td>7</td><td>fw_soft_clipped_start</td><td>number of bases soft clipped from the start of the forward-oriented read</td><td>int</td></tr>
-<tr><td>8</td><td>fw_soft_clipped_end</td><td>number of bases soft clipped from the end of the forward-oriented read</td><td>int</td></tr>
-<tr><td>9</td><td>read_length</td><td>total length of the read</td><td>int</td></tr>
-<tr><td>10</td><td>mod_qual</td><td>probability of the base modification in the next column</td><td>int</td></tr>
-<tr><td>11</td><td>mod_code</td><td>base modification code from the MM tag</td><td>str</td></tr>
-<tr><td>12</td><td>base_qual</td><td>basecall quality score (phred)</td><td>int</td></tr>
-<tr><td>13</td><td>ref_kmer</td><td>reference 5-mer sequence context (center base is aligned base), '.' if unmapped</td><td>str</td></tr>
-<tr><td>14</td><td>query_kmer</td><td>read 5-mer sequence context (center base is aligned base)</td><td>str</td></tr>
-<tr><td>15</td><td>canonical_base</td><td>canonical base from the query sequence, from the MM tag</td><td>str</td></tr>
+<tr><td>7</td><td>ref_mod_strand</td><td>strand of the reference with the base modification, or '.' if unmapped</td><td>str</td></tr>
+<tr><td>8</td><td>fw_soft_clipped_start</td><td>number of bases soft clipped from the start of the forward-oriented read</td><td>int</td></tr>
+<tr><td>9</td><td>fw_soft_clipped_end</td><td>number of bases soft clipped from the end of the forward-oriented read</td><td>int</td></tr>
+<tr><td>10</td><td>read_length</td><td>total length of the read</td><td>int</td></tr>
+<tr><td>11</td><td>mod_qual</td><td>probability of the base modification in the next column</td><td>int</td></tr>
+<tr><td>12</td><td>mod_code</td><td>base modification code from the MM tag</td><td>str</td></tr>
+<tr><td>13</td><td>base_qual</td><td>basecall quality score (phred)</td><td>int</td></tr>
+<tr><td>14</td><td>ref_kmer</td><td>reference 5-mer sequence context (center base is aligned base), '.' if unmapped</td><td>str</td></tr>
+<tr><td>15</td><td>query_kmer</td><td>read 5-mer sequence context (center base is aligned base)</td><td>str</td></tr>
+<tr><td>16</td><td>canonical_base</td><td>canonical base from the query sequence, from the MM tag</td><td>str</td></tr>
+<tr><td>16</td><td>modified_primary_base</td><td>primary sequence base with the modification</td><td>str</td></tr>
 </tbody></table>
 </div>
 <h2 id="example-usages"><a class="header" href="#example-usages">Example usages:</a></h2>