Shogo Ohta

Built-in readline support

1

Currently, Trenchman does not have built-in support for readline-like features, like line editing or history search. The installation instruction suggests using the tool with `rlwrap`, but for more usability, it...

Mustache spec [v1.2.0](https://github.com/mustache/spec/releases/tag/v1.2.0) added a new feature [inheritance](https://github.com/mustache/spec/blob/master/specs/~inheritance.yml). Due to this change, the latest spec tests would fail with the current Pogonos, so we cannot update the test suit for...

Currently, the VCF reader/writer aren't supporting `##META` meta info line, which is [mentioned in the spec v4.3](https://github.com/samtools/hts-specs/blob/ce7f2a61fca5e9f906caa72128cade0065b8361a/VCFv4.3.tex#L233-L236). They don't throw an error when encountering such lines, but silently process them...

(pinpoint <predicate> <input>) fails

3

```clj => (pinpoint integer? :foo) [PINPOINTER] Failed to analyze the spec errors, and will fall back to s/explain-printer val: :foo fails predicate: :clojure.spec.alpha/unknown nil => (pinpoint integer? :foo {:fallback-on-error false})...

(pinpoint (s/& ...) <input>) fails

2

```clj => (pinpoint (s/& integer? even?) [1]) [PINPOINTER] Failed to analyze the spec errors, and will fall back to s/explain-printer In: [0] val: 1 fails predicate: even? nil => (pinpoint...

```clj => (pinpoint (s/coll-of integer?) [:foo]) [PINPOINTER] Failed to analyze the spec errors, and will fall back to s/explain-printer In: [0] val: :foo fails predicate: integer? nil => (pinpoint (s/coll-of...

```clj => (s/def ::x integer?) :user/x => (pinpoint (s/keys* :req [::x]) [::x :foo]) [PINPOINTER] Failed to analyze the spec errors, and will fall back to s/explain-printer In: [:user/x] val: :foo...

According to [JLS 15.25](https://docs.oracle.com/javase/specs/jls/se11/html/jls-15.html#jls-15.25), typing the conditional operator never fails unless it includes an invocation of a void method. However, the current implementation throws `VerifyError` when the second and third...

cram: interpretation of "unmapped" flag in a pseudocode seems incorrect

1

In the CRAM specification, Section 10.6 has the following pseudocode: ``` procedure DecodeRecord ... if (BF AND 4) != 0 then DecodeMappedRead else DecodeUnmappedRead end if end procedure ``` I...