Inconsistent default values for samplingDepth in wiki and codebase

[ajw725]

The Alignment Track wiki page says that the default for samplingDepth is 100. (yes, with the period).

In alignmentContainer.js, the default appears to be 1000, not 100. It looks like it used to be 100 several years ago, but was changed to 1000 in 2019. It's also 1000 in Ga4ghAlignmentReader.

In bamUtils.js, the default depth appears to be 500. It was set to 1000 on 7/18/19 along with the one in AlignmentContainer, but then it appears to have been changed again a few days later.

This started out as just a request to update the wiki, but then I got curious about the different values in the code. I'm not familiar with the codebase, but I was poking around a little, and it seems like the same config object gets passed to both BamUtils.setReaderDefaults and new AlignmentContainer (e.g. from BamReader). Does this mean the same user-provided samplingDepth would potentially override both of these things, but if the user doesn't provide a value, they each have different defaults for that parameter?

[jrobinso]

The user setting will override any defaults. Different readers can have different defaults, in particular the now defunct GA4GH reader, however I am not sure why bamUtils and alignmentContainer have separate variables for this. I will investigate, thanks for the forensics work.

…

On Fri, Apr 21, 2023 at 8:33 PM Andrew Weinstein ***@***.***> wrote: The Alignment Track wiki page <https://github.com/igvteam/igv.js/wiki/Alignment-Track> says that the default for samplingDepth is 100. (yes, with the period). In alignmentContainer.js <https://github.com/igvteam/igv.js/blob/master/js/bam/alignmentContainer.js#L49>, the default appears to be 1000, not 100. It looks like it used to be 100 several years ago, but was changed to 1000 <16a5082> in 2019. It's also 1000 in Ga4ghAlignmentReader. In bamUtils.js <https://github.com/igvteam/igv.js/blob/master/js/bam/bamUtils.js#L49>, the default depth appears to be 500. It was set to 1000 on 7/18/19 along with the one in AlignmentContainer, but then it appears to have been changed again <443d857> a few days later. This started out as just a request to update the wiki, but then I got curious about the different values in the code. I'm not familiar with the codebase, but I was poking around a little, and it seems like the same config object gets passed to both BamUtils.setReaderDefaults and new AlignmentContainer. Does this mean the same user-provided samplingDepth would potentially override both of these things, but if the user doesn't provide a value, they each have different defaults for that parameter? — Reply to this email directly, view it on GitHub <#1631>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAHD2HES3ORECJTLACKW4PTXCMRPDANCNFSM6AAAAAAXHOU3RI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>