---
name: "loadPulses"
section: "1"
platform: "linux"
package: "blasr"
version: "5.3+0-1"
release: "Debian 9 (Stretch)"
platforms: ["linux"]
url: "https://new.carta.tech/loadPulses"
---

# loadPulses(1)

load sequencing pulse information

## NAME

loadPulses - load sequencing pulse information

## SYNOPSIS

**loadPulses** *basFileName* *cmpFileName* \[*options*\]

## DESCRIPTION

**loadPulses** loads sequencing pulse information such as inter-pulse distance or quality information into the cmp.h5 file. This allows one to analyze kinetic and quality information by alignment column.

## OPTIONS

- *basFileName*

  The input {bas,pls}.h5 or input.fofn.

- *cmpFileName*

  The cmp.h5 file to load pulse information into.

- **-metrics** *value*

  A comma separated list of metrics (with no spaces).

  - Valid options are:

    WhenStarted, QualityValue, InsertionQV, MergeQV, DeletionQV, DeletionTag, SubstitutionTag, SubstitutionQV, PreBaseFrames, IPD, StartFrame, PulseWidth, WidthInFrames, Light, pkmid, ClassifierQV, PulseIndex

  - Default options are:

    QualityValue, ClassifierQV, StartFrame, PulseWidth, WidthInFrames, pkmid, IPD

- **-failOnMissingData**

  Exit if any data fields are missing from the bas.h5 or pls.h5 input that are required to load a metric. Defualt is a warning.

- **-byread**

  Load pulse information by read rather than buffering metrics.

- **-bymetric**

  Load pulse information by metric rather than by read. This uses more memory than **-byread**, but can be faster.

- **-maxElements** *value*

  Set a limit on the size of pls/bas file to buffer in with **-bymetric** (default value: maximum int). Use **-byread** if the limit is exceeded.

- **-maxMemory** *value*

  Set a limit (in GB) on the memory to buffer data with **-bymetric** (default value: 4 GB). Use **-byread** if the limit is exceeded.

- **-metaNElements** *value*

  Set number of elements in meta data cache for reading bas/bax/pls.h5 file.

- **-rawNElements***value*

  Set number of elements in raw data cache for reading the bas/bax/pls.h5 file.

- **-rawChunkSize** *value*

  Set chunk size of raw data cache for reading the bas/bax/pls.h5 file.

## SEE ALSO

[**blasr**(1)](/blasr/1.md) [**pls2fasta**(1)](/pls2fasta/1.md) [**samFilter**(1)](/samFilter/1.md) [**samtoh5**(1)](/samtoh5/1.md) [**samtom4**(1)](/samtom4/1.md) [**sawriter**(1)](/sawriter/1.md) [**sdpMatcher**(1)](/sdpMatcher/1.md) [**toAfg**(1)](/toAfg/1.md)