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add docs for ex-zd
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docs/commands.md

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@@ -27,7 +27,7 @@ slow5curl get [OPTIONS] https://url/to/file1.blow5 --list readids.txt
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* `-c, --compress compression_type`:<br/>
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Specifies the compression method used for BLOW5 output. `compression_type` can be `none` for uncompressed binary; `zlib` for zlib-based (also known as gzip or DEFLATE) compression; or `zstd` for Z-standard-based compression [default value: zlib]. This option is only valid for BLOW5. `zstd` will only function if slow5curl has been built with zstd support which is turned off by default.
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* `-s, --sig-compress compression_type`:<br/>
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Specifies the raw signal compression method used for BLOW5 output. `compression_type` can be `none` for uncompressed raw signal or `svb-zd` to compress the raw signal using StreamVByte zig-zag delta [default value: svb-zd]. Note that record compression (-c option above) is still applied on top of the compressed signal. Signal compression with svb-zd and record compression with zstd is similar to ONT's vbz. zstd+svb-zd offers slightly smaller file size and slightly better performance compared to the default zlib+svb-zd, however, will be less portable.
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Specifies the raw signal compression method used for BLOW5 output. `compression_type` can be `none` for uncompressed raw signal, `svb-zd` to compress the raw signal using StreamVByte zig-zag delta, `ex-zd` (slow5curl v0.4.0 onwards) for exception coding [default value: svb-zd]. `ex-zd` offers a better compression ratio to svb-zd. Note that record compression (-c option above) is still applied on top of the compressed signal. Signal compression with svb-zd and record compression with zstd is similar to ONT's vbz. zstd+svb-zd offers slightly smaller file size and slightly better performance compared to the default zlib+svb-zd, however, will be less portable.
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* `-t, --threads INT`:<br/>
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Number of threads (connections) [default value: 128]. As these threads are for network access, the number of threads can be much larger than the number of CPU threads available on the system. The max number of threads will typically depend on the request limit of the server. For example, we may go up to 512 threads, but if the server only allows 128 requests at a time per client, we will be limited by the latter.
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* `-K, --batchsize`:<br/>

src_tool/cmd.h

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@@ -75,7 +75,8 @@ extern "C" {
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" zstd - Z standard \n" \
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"SIG_MTD:\n" \
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" none - no special signal compression\n" \
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" svb-zd - StreamVByte with zig-zag delta \n\n" \
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" svb-zd - StreamVByte with zig-zag delta \n" \
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" ex-zd - exception with zig-zag delta\n\n"
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#define HELP_DOCS \
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"See https://slow5.bioinf.science/slow5curl for a detailed description of these command-line options.\n"

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