Fix/add doc string #282
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Fix/add doc string #282
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Codecov Report
@@ Coverage Diff @@
## master #282 +/- ##
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- Coverage 88.86% 88.84% -0.02%
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Files 79 79
Lines 6772 6778 +6
Branches 475 475
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+ Hits 6018 6022 +4
- Misses 279 281 +2
Partials 475 475
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alumi
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Oct 11, 2023
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Thank you for adding the docstrings, @niyarin!
Adding documentation across the entire library must be a tough task. 🙏
Overall, I find it good, but I thought there's room for improvement in a few areas.
I believe it's a great opportunity to reduce the psychological barriers to using the library for new users 🉐
- Enclose symbols like arguments in backticks ` `.
- In cases like the following, provide more detailed information on return values:
- When the implementation is not immediately clear.
- When it's not intuitive from the namespace and function names.
- When it might require referring to tests.
- Address some grammatical issues, including
- punctuation
- capitalization
- third-person singular '-s'
- missing 'a' or 'the'
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Oct 20, 2023
src/cljam/io/bam_index/common.clj
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| (def ^:const linear-index-shift 14) | ||
| (def ^:const linear-index-depth 5) | ||
| (def ^:const linear-index-shift | ||
| "Minimum shift size for searching binnning." |
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Suggested change
| "Minimum shift size for searching binnning." | |
| "Minimum shift size for searching binning." |
src/cljam/io/fasta/writer.clj
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| (defn writer [f {:keys [cols create-index?] | ||
| :or {cols 80 create-index? true}}] | ||
| (defn writer | ||
| "Returns an open `cljam.io.fasta.writer.FATAWriter` of `f`. |
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| "Returns an open `cljam.io.fasta.writer.FATAWriter` of `f`. | |
| "Returns an open `cljam.io.fasta.writer.FASTAWriter` of `f`. |
src/cljam/io/sam/util/quality.clj
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| (defn phred-bytes->fastq | ||
| "Convertsphred bytes to fastq quality string." |
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| "Convertsphred bytes to fastq quality string." | |
| "Converts phred bytes to fastq quality string." |
src/cljam/io/vcf/reader.clj
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| @@ -119,6 +120,7 @@ | |||
| v)])) | |||
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| (defn load-meta-info | |||
| "Reads from rdr and parases them as meta-info." | |||
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| "Reads from rdr and parases them as meta-info." | |
| "Reads from `rdr` and parses them as meta-info." |
src/cljam/io/vcf/reader.clj
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| [line] | ||
| (cstr/split (subs line 1) #"\t")) | ||
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| (defn load-header | ||
| "Reads from `rdr` and parases them as header." |
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| "Reads from `rdr` and parases them as header." | |
| "Reads from `rdr` and parses them as header." |
src/cljam/util/chromosome.clj
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| @@ -4,6 +4,8 @@ | |||
| [proton.core :as proton])) | |||
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| (defn normalize-name | |||
| "Converts characters ',' or '.' in chromesome name to '_' | |||
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| "Converts characters ',' or '.' in chromesome name to '_' | |
| "Converts characters ',' or '.' in chromosome name to '_' |
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Thank you for reviewing. |
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