BamFlags - SeqAn API Documentation

# Enum BamFlags
Shortcuts to the bitmask flags for BAM/SAM files.

Defined in | <seqan/bam_io.h>
Signature | `enum BamFlags;`

## Enum Values

`BAM_FLAG_MULTIPLE = 0x0001` | Template has multiple fragments in sequencing.
`BAM_FLAG_ALL_PROPER = 0x0002` | All fragments in the template are properly mapped.
`BAM_FLAG_UNMAPPED = 0x0004` | This fragment is unmapped.
`BAM_FLAG_NEXT_UNMAPPED = 0x0008` | Next fragment in template is unmapped.
`BAM_FLAG_RC = 0x0010` | Fragment is reverse-complemented.
`BAM_FLAG_NEXT_RC = 0x0020` | Next fragment in template is reverse-complemented.
`BAM_FLAG_FIRST = 0x0040` | This fragment is the first one in its template.
`BAM_FLAG_LAST = 0x0080` | This fragment is the last one in its template (second in case of paired sequencing).
`BAM_FLAG_SECONDARY = 0x0100` | Secondary alignment.
`BAM_FLAG_QC_NO_PASS = 0x0200` | Does not pass quality controls.
`BAM_FLAG_DUPLICATE = 0x0400` | PCR or optical duplicate.

#### Dox Sources

    /*!
     * @enum BamFlags
     *
     * @headerfile <seqan/bam_io.h>
     *
     * @brief Shortcuts to the bitmask flags for BAM/SAM files.
     *
     * @signature enum BamFlags;
     *
     * @val BamFlags BAM_FLAG_MULTIPLE = 0x0001;
     *
     * @brief Template has multiple fragments in sequencing.
     *
     * @val BamFlags BAM_FLAG_ALL_PROPER = 0x0002;
     *
     * @brief All fragments in the template are properly mapped.
     *
     * @val BamFlags BAM_FLAG_UNMAPPED = 0x0004;
     *
     * @brief This fragment is unmapped.
     *
     * @val BamFlags BAM_FLAG_NEXT_UNMAPPED = 0x0008;
     *
     * @brief Next fragment in template is unmapped.
     *
     * @val BamFlags BAM_FLAG_RC = 0x0010;
     *
     * @brief Fragment is reverse-complemented.
     *
     * @val BamFlags BAM_FLAG_NEXT_RC = 0x0020;
     *
     * @brief Next fragment in template is reverse-complemented.
     *
     * @val BamFlags BAM_FLAG_FIRST = 0x0040;
     *
     * @brief This fragment is the first one in its template.
     *
     * @val BamFlags BAM_FLAG_LAST = 0x0080;
     *
     * @brief This fragment is the last one in its template (second in case of
     *        paired sequencing).
     *
     * @val BamFlags BAM_FLAG_SECONDARY = 0x0100;
     *
     * @brief Secondary alignment.
     *
     * @val BamFlags BAM_FLAG_QC_NO_PASS = 0x0200;
     *
     * @brief Does not pass quality controls.
     *
     * @val BamFlags BAM_FLAG_DUPLICATE = 0x0400;
     *
     * @brief PCR or optical duplicate.
     */