add adapter in read simulation

[yunfeiguo]

• [x] RES-362
• [x] Blocking PRs: ADD HERE IF ANY
• People
  • [x] Reviewers (>=1): @bayolau @marghoob
  • [x] Merger (>=1): @bayolau @marghoob
  • [x] FYI:
• [ ] Tests (Unit, Workflow, ITL & Gherkin) are passing

Summary

• edited pom.xml and added some dependency jars to repo so that development can be conveniently done locally
• some refactoring: primarily renaming some variables for easier understanding; adding some comments
• implemented polymerase read simulation independent of current subread simulation (via overloading). a full polymerase read without errors is assembled, consisting of multiple adapters, and inserts, then errors are simulated by iterating over the template. This avoids the issue of missing context at ends of subreads. But the ends of a polymerase read will still miss leftFlank + rightFlank bp.
• remaining issues tests passed using pure java on my laptop. However, the jar file cannot be run directly on Pleasanton server. While I'm addressing this issue, please review the code.

Sorry for being late, I could have been faster if I did not spend too much time on understanding model file loading. Thanks!

[bayolau]

please remove all jar binaries from this pull request

[bayolau]

in general when multiple people are working on the codebase, we don't want to rename/refactor anything unless necessary. This will create merge problem

[yunfeiguo]

Cool. Thanks!

I will revert the changes in pom.xml. Also the refactoring need to be reverted too?

[bayolau]

Let me stress that your changes are great and are much needed. It's my bad that I didn't say anything before. Usually the refactoring commit should be pure cosmetic (without any functionality change) after a merge point but before branching off.

Since we got 3 active branches going, let's keep your changes to see if the other collide with yours (or you can see if fragment and slen will merge cleanly to yours.

[yunfeiguo]

Thanks! How does it look now?

On Wed, Oct 26, 2016 at 7:34 PM, bayolau notifications@github.com wrote:

@bayolau commented on this pull request.

In src/main/java/com/bina/lrsim/pb/Spec.java https://github.com/bioinform/longislnd/pull/23#pullrequestreview-5982877 :

@@ -122,6 +141,26 @@ public static Spec fromReadType(final String readType) { return UnknownSpec; }

• public boolean isPolymeraseReadFlag() {
• return polymeraseReadFlag;
• }
• public byte[] getAdapterSequence() {
• return adapterSequence;
• }
• public void setPolymeraseReadFlag(final String outputPolymeraseRead) {
• if (outputPolymeraseRead.equals("True")) {

this can be a bit dangerous since it's one-sided, let's try to use a boolean paramter here such that this.polymeraseReadFlag = outputPolymeraseRead

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[bayolau]

+1 thanks @yunfeiguo